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‎.gitignore

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@@ -6,3 +6,4 @@ cellranger_related/cellranger-9.0.1/
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cellranger_related/cellranger-atac-2.1.0/
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sequencing_results/
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h5ad_files/
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*.mro

‎cellranger_related/cellranger_code/cellranger_count/job.8681809.out

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‎cellranger_related/cellranger_code/cellranger_count/job.8681858.out

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‎cellranger_related/cellranger_code/cellranger_count/job.8682052.err

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@@ -4,4 +4,8 @@ Could not find a 10x cloud token in the default user directory. In order to ena
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tar: Removing leading `/' from member names
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Could not find a 10x cloud token in the default user directory. In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.
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tar: Removing leading `/' from member names
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Could not find a 10x cloud token in the default user directory. In order to enable cell annotation, run cellranger cloud auth setup, or please supply a --tenx-cloud-token-path argument.

‎cellranger_related/cellranger_code/cellranger_count/job.8682052.out

+129
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‎cellranger_related/cellranger_code/velocyto/job.8681948.out

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Original file line numberDiff line numberDiff line change
@@ -1835,3 +1835,56 @@ A00709:866:HHG3WDSXC:2:2561:9408:20353 0 12 17841724 255 145M3507778N6M * 0 0 AG
18351835
2025-02-28 15:32:39,618 - DEBUG - Counting for batch 35, containing 100 cells and 2715872 reads
18361836
2025-02-28 15:34:25,461 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:35:27,968 - DEBUG - Counting for batch 36, containing 100 cells and 2841034 reads
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2025-02-28 15:37:19,221 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:38:10,237 - DEBUG - Read first 160 million reads
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2025-02-28 15:38:19,907 - DEBUG - Counting for batch 37, containing 100 cells and 2609390 reads
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2025-02-28 15:40:01,210 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:41:05,559 - DEBUG - Counting for batch 38, containing 100 cells and 2947618 reads
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2025-02-28 15:43:00,173 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:44:12,115 - DEBUG - Counting for batch 39, containing 100 cells and 2850192 reads
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2025-02-28 15:45:58,419 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:46:29,407 - DEBUG - Read first 170 million reads
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2025-02-28 15:47:01,942 - DEBUG - Counting for batch 40, containing 100 cells and 2435587 reads
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2025-02-28 15:48:37,327 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:49:34,695 - DEBUG - Counting for batch 41, containing 100 cells and 2554449 reads
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2025-02-28 15:51:12,848 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:52:16,717 - DEBUG - Read first 180 million reads
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2025-02-28 15:52:20,327 - DEBUG - Counting for batch 42, containing 100 cells and 2937757 reads
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2025-02-28 15:54:13,639 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:55:19,500 - DEBUG - Counting for batch 43, containing 100 cells and 2595278 reads
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2025-02-28 15:56:56,923 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:57:59,701 - DEBUG - Counting for batch 44, containing 100 cells and 2725084 reads
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2025-02-28 15:59:42,044 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:00:25,203 - DEBUG - Read first 190 million reads
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2025-02-28 16:00:46,860 - DEBUG - Counting for batch 45, containing 100 cells and 2646798 reads
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2025-02-28 16:02:23,655 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:03:32,881 - DEBUG - Counting for batch 46, containing 100 cells and 2754103 reads
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2025-02-28 16:05:14,733 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:06:17,848 - DEBUG - Counting for batch 47, containing 100 cells and 2341669 reads
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2025-02-28 16:07:49,724 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:08:23,489 - DEBUG - Read first 200 million reads
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2025-02-28 16:08:46,977 - DEBUG - Counting for batch 48, containing 100 cells and 2452316 reads
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2025-02-28 16:10:22,991 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:11:30,909 - DEBUG - Counting for batch 49, containing 100 cells and 2913416 reads
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2025-02-28 16:13:23,704 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:14:28,484 - DEBUG - Read first 210 million reads
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2025-02-28 16:14:30,435 - DEBUG - Counting for batch 50, containing 100 cells and 2899364 reads
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2025-02-28 16:16:21,021 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:17:31,140 - DEBUG - Counting for batch 51, containing 100 cells and 3218150 reads
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2025-02-28 16:19:36,186 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:20:48,406 - DEBUG - Counting for batch 52, containing 100 cells and 2696378 reads
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2025-02-28 16:22:28,157 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:23:10,375 - DEBUG - Read first 220 million reads
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2025-02-28 16:23:45,103 - DEBUG - Counting for batch 53, containing 100 cells and 2927250 reads
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2025-02-28 16:25:37,862 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:26:43,275 - DEBUG - Counting for batch 54, containing 100 cells and 2345133 reads
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2025-02-28 16:28:09,448 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:29:20,553 - DEBUG - Read first 230 million reads
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2025-02-28 16:29:21,203 - DEBUG - Counting for batch 55, containing 100 cells and 2943748 reads
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2025-02-28 16:31:09,269 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:32:15,297 - DEBUG - Counting for batch 56, containing 100 cells and 2523416 reads
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2025-02-28 16:33:50,059 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:35:01,892 - DEBUG - Counting for batch 57, containing 100 cells and 2913328 reads
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2025-02-28 16:36:49,880 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:37:41,364 - DEBUG - Read first 240 million reads
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2025-02-28 16:38:02,175 - DEBUG - Counting for batch 58, containing 100 cells and 3058500 reads

‎cellranger_related/cellranger_code/velocyto/job.8681949.out

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@@ -5775,3 +5775,111 @@
57755775
2025-02-28 15:34:57,513 - DEBUG - Read first 260 million reads
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2025-02-28 15:35:08,045 - DEBUG - Counting for batch 93, containing 100 cells and 1845648 reads
57775777
2025-02-28 15:35:53,466 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:36:32,561 - DEBUG - Counting for batch 94, containing 100 cells and 1978708 reads
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2025-02-28 15:37:16,792 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:37:53,613 - DEBUG - Counting for batch 95, containing 100 cells and 1731002 reads
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2025-02-28 15:38:31,853 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:39:04,489 - DEBUG - Counting for batch 96, containing 100 cells and 1563406 reads
5783+
2025-02-28 15:39:40,420 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
5784+
2025-02-28 15:40:00,547 - DEBUG - Read first 270 million reads
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2025-02-28 15:40:10,756 - DEBUG - Counting for batch 97, containing 100 cells and 1616017 reads
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2025-02-28 15:40:47,008 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:41:19,880 - DEBUG - Counting for batch 98, containing 100 cells and 1693202 reads
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2025-02-28 15:41:57,935 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:42:33,781 - DEBUG - Counting for batch 99, containing 100 cells and 1866652 reads
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2025-02-28 15:43:16,420 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:43:50,219 - DEBUG - Counting for batch 100, containing 100 cells and 1682255 reads
5792+
2025-02-28 15:44:29,981 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
5793+
2025-02-28 15:44:51,303 - DEBUG - Read first 280 million reads
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2025-02-28 15:45:03,002 - DEBUG - Counting for batch 101, containing 100 cells and 1810727 reads
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2025-02-28 15:45:44,042 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:46:17,460 - DEBUG - Counting for batch 102, containing 100 cells and 1799969 reads
5797+
2025-02-28 15:46:58,219 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:47:34,501 - DEBUG - Counting for batch 103, containing 100 cells and 1998931 reads
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2025-02-28 15:48:19,806 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:48:57,706 - DEBUG - Counting for batch 104, containing 100 cells and 1912649 reads
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2025-02-28 15:49:42,102 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:50:01,882 - DEBUG - Read first 290 million reads
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2025-02-28 15:50:18,289 - DEBUG - Counting for batch 105, containing 100 cells and 1785554 reads
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2025-02-28 15:50:59,124 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:51:30,734 - DEBUG - Counting for batch 106, containing 100 cells and 1571433 reads
5806+
2025-02-28 15:52:05,013 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:52:38,909 - DEBUG - Counting for batch 107, containing 100 cells and 1717964 reads
5808+
2025-02-28 15:53:18,000 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:53:52,313 - DEBUG - Counting for batch 108, containing 100 cells and 1760971 reads
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2025-02-28 15:54:33,023 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:54:50,218 - DEBUG - Read first 300 million reads
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2025-02-28 15:55:08,685 - DEBUG - Counting for batch 109, containing 100 cells and 1864774 reads
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2025-02-28 15:55:53,004 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:56:27,502 - DEBUG - Counting for batch 110, containing 100 cells and 1828098 reads
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2025-02-28 15:57:12,890 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:57:48,763 - DEBUG - Counting for batch 111, containing 100 cells and 1831734 reads
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2025-02-28 15:58:32,703 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 15:59:14,620 - DEBUG - Counting for batch 112, containing 100 cells and 1772583 reads
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2025-02-28 15:59:57,629 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:00:15,950 - DEBUG - Read first 310 million reads
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2025-02-28 16:00:35,192 - DEBUG - Counting for batch 113, containing 100 cells and 1482878 reads
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2025-02-28 16:01:09,807 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:01:50,740 - DEBUG - Counting for batch 114, containing 100 cells and 1874311 reads
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2025-02-28 16:02:39,552 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:03:20,119 - DEBUG - Counting for batch 115, containing 100 cells and 1712573 reads
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2025-02-28 16:04:03,270 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:04:45,100 - DEBUG - Counting for batch 116, containing 100 cells and 1795115 reads
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2025-02-28 16:05:27,953 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:05:44,617 - DEBUG - Read first 320 million reads
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2025-02-28 16:06:07,940 - DEBUG - Counting for batch 117, containing 100 cells and 1804999 reads
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2025-02-28 16:06:53,616 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:07:32,917 - DEBUG - Counting for batch 118, containing 100 cells and 1910234 reads
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2025-02-28 16:08:23,425 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:09:06,718 - DEBUG - Counting for batch 119, containing 100 cells and 2056455 reads
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2025-02-28 16:09:55,073 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:10:29,621 - DEBUG - Read first 330 million reads
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2025-02-28 16:10:36,072 - DEBUG - Counting for batch 120, containing 100 cells and 1940803 reads
5838+
2025-02-28 16:11:21,084 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:11:59,362 - DEBUG - Counting for batch 121, containing 100 cells and 1871399 reads
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2025-02-28 16:12:42,980 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:13:18,226 - DEBUG - Counting for batch 122, containing 100 cells and 1838641 reads
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2025-02-28 16:14:01,215 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:14:42,888 - DEBUG - Counting for batch 123, containing 100 cells and 1978571 reads
5844+
2025-02-28 16:15:27,037 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:15:49,326 - DEBUG - Read first 340 million reads
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2025-02-28 16:16:02,828 - DEBUG - Counting for batch 124, containing 100 cells and 1615401 reads
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2025-02-28 16:16:38,371 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:17:14,400 - DEBUG - Counting for batch 125, containing 100 cells and 1853066 reads
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2025-02-28 16:17:56,245 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:18:35,349 - DEBUG - Counting for batch 126, containing 100 cells and 2005785 reads
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2025-02-28 16:19:21,377 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:19:58,163 - DEBUG - Counting for batch 127, containing 100 cells and 1996109 reads
5853+
2025-02-28 16:20:44,106 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
5854+
2025-02-28 16:20:59,275 - DEBUG - Read first 350 million reads
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2025-02-28 16:21:20,824 - DEBUG - Counting for batch 128, containing 100 cells and 1966028 reads
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2025-02-28 16:22:06,127 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:22:39,703 - DEBUG - Counting for batch 129, containing 100 cells and 1739330 reads
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2025-02-28 16:23:19,942 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:23:57,755 - DEBUG - Counting for batch 130, containing 100 cells and 1919197 reads
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2025-02-28 16:24:42,037 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:25:14,996 - DEBUG - Read first 360 million reads
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2025-02-28 16:25:19,639 - DEBUG - Counting for batch 131, containing 100 cells and 1985749 reads
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2025-02-28 16:26:05,995 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:26:41,387 - DEBUG - Counting for batch 132, containing 100 cells and 1740361 reads
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2025-02-28 16:27:22,211 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:27:56,081 - DEBUG - Counting for batch 133, containing 100 cells and 1803790 reads
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2025-02-28 16:28:37,200 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:29:15,974 - DEBUG - Counting for batch 134, containing 100 cells and 2113472 reads
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2025-02-28 16:30:03,290 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:30:29,996 - DEBUG - Read first 370 million reads
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2025-02-28 16:30:40,721 - DEBUG - Counting for batch 135, containing 100 cells and 1781011 reads
5872+
2025-02-28 16:31:22,342 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:31:57,055 - DEBUG - Counting for batch 136, containing 100 cells and 1834927 reads
5874+
2025-02-28 16:32:38,913 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:33:16,109 - DEBUG - Counting for batch 137, containing 100 cells and 1993476 reads
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2025-02-28 16:34:01,741 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
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2025-02-28 16:34:40,356 - DEBUG - Counting for batch 138, containing 100 cells and 1874090 reads
5878+
2025-02-28 16:35:25,339 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
5879+
2025-02-28 16:35:44,839 - DEBUG - Read first 380 million reads
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2025-02-28 16:35:59,764 - DEBUG - Counting for batch 139, containing 100 cells and 1635478 reads
5881+
2025-02-28 16:36:37,588 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
5882+
2025-02-28 16:37:12,127 - DEBUG - Counting for batch 140, containing 100 cells and 1855184 reads
5883+
2025-02-28 16:37:53,279 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions
5884+
2025-02-28 16:38:31,434 - DEBUG - Counting for batch 141, containing 100 cells and 1884847 reads
5885+
2025-02-28 16:39:16,066 - DEBUG - 0 reads not considered because fully enclosed in repeat masked regions

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