Job ID = 14171980 SRX = SRX7889139 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27963455 spots for SRR11283129/SRR11283129.sra Written 27963455 spots for SRR11283129/SRR11283129.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172599 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:51:15 27963455 reads; of these: 27963455 (100.00%) were paired; of these: 8127659 (29.07%) aligned concordantly 0 times 17537265 (62.71%) aligned concordantly exactly 1 time 2298531 (8.22%) aligned concordantly >1 times ---- 8127659 pairs aligned concordantly 0 times; of these: 2031210 (24.99%) aligned discordantly 1 time ---- 6096449 pairs aligned 0 times concordantly or discordantly; of these: 12192898 mates make up the pairs; of these: 9960942 (81.69%) aligned 0 times 1592638 (13.06%) aligned exactly 1 time 639318 (5.24%) aligned >1 times 82.19% overall alignment rate Time searching: 00:51:16 Overall time: 00:51:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 36 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2345852 / 20733751 = 0.1131 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 14:55:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:55:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:55:58: 1000000 INFO @ Sat, 11 Dec 2021 14:56:07: 2000000 INFO @ Sat, 11 Dec 2021 14:56:15: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 14:56:20: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:56:20: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:56:24: 4000000 INFO @ Sat, 11 Dec 2021 14:56:30: 1000000 INFO @ Sat, 11 Dec 2021 14:56:34: 5000000 INFO @ Sat, 11 Dec 2021 14:56:41: 2000000 INFO @ Sat, 11 Dec 2021 14:56:44: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 11 Dec 2021 14:56:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:56:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:56:51: 3000000 INFO @ Sat, 11 Dec 2021 14:56:54: 7000000 INFO @ Sat, 11 Dec 2021 14:57:02: 4000000 INFO @ Sat, 11 Dec 2021 14:57:03: 1000000 INFO @ Sat, 11 Dec 2021 14:57:06: 8000000 INFO @ Sat, 11 Dec 2021 14:57:14: 5000000 INFO @ Sat, 11 Dec 2021 14:57:15: 2000000 INFO @ Sat, 11 Dec 2021 14:57:17: 9000000 INFO @ Sat, 11 Dec 2021 14:57:25: 6000000 INFO @ Sat, 11 Dec 2021 14:57:27: 3000000 INFO @ Sat, 11 Dec 2021 14:57:29: 10000000 INFO @ Sat, 11 Dec 2021 14:57:37: 7000000 INFO @ Sat, 11 Dec 2021 14:57:39: 4000000 INFO @ Sat, 11 Dec 2021 14:57:40: 11000000 INFO @ Sat, 11 Dec 2021 14:57:48: 8000000 INFO @ Sat, 11 Dec 2021 14:57:51: 5000000 INFO @ Sat, 11 Dec 2021 14:57:52: 12000000 INFO @ Sat, 11 Dec 2021 14:58:00: 9000000 INFO @ Sat, 11 Dec 2021 14:58:03: 13000000 INFO @ Sat, 11 Dec 2021 14:58:04: 6000000 INFO @ Sat, 11 Dec 2021 14:58:11: 10000000 INFO @ Sat, 11 Dec 2021 14:58:15: 14000000 INFO @ Sat, 11 Dec 2021 14:58:16: 7000000 INFO @ Sat, 11 Dec 2021 14:58:23: 11000000 INFO @ Sat, 11 Dec 2021 14:58:26: 15000000 INFO @ Sat, 11 Dec 2021 14:58:28: 8000000 INFO @ Sat, 11 Dec 2021 14:58:34: 12000000 INFO @ Sat, 11 Dec 2021 14:58:38: 16000000 INFO @ Sat, 11 Dec 2021 14:58:40: 9000000 INFO @ Sat, 11 Dec 2021 14:58:46: 13000000 INFO @ Sat, 11 Dec 2021 14:58:49: 17000000 INFO @ Sat, 11 Dec 2021 14:58:53: 10000000 INFO @ Sat, 11 Dec 2021 14:58:57: 14000000 INFO @ Sat, 11 Dec 2021 14:59:01: 18000000 INFO @ Sat, 11 Dec 2021 14:59:05: 11000000 INFO @ Sat, 11 Dec 2021 14:59:09: 15000000 INFO @ Sat, 11 Dec 2021 14:59:12: 19000000 INFO @ Sat, 11 Dec 2021 14:59:17: 12000000 INFO @ Sat, 11 Dec 2021 14:59:20: 16000000 INFO @ Sat, 11 Dec 2021 14:59:24: 20000000 INFO @ Sat, 11 Dec 2021 14:59:29: 13000000 INFO @ Sat, 11 Dec 2021 14:59:31: 17000000 INFO @ Sat, 11 Dec 2021 14:59:35: 21000000 INFO @ Sat, 11 Dec 2021 14:59:41: 14000000 INFO @ Sat, 11 Dec 2021 14:59:43: 18000000 INFO @ Sat, 11 Dec 2021 14:59:46: 22000000 INFO @ Sat, 11 Dec 2021 14:59:53: 15000000 INFO @ Sat, 11 Dec 2021 14:59:55: 19000000 INFO @ Sat, 11 Dec 2021 14:59:58: 23000000 INFO @ Sat, 11 Dec 2021 15:00:05: 16000000 INFO @ Sat, 11 Dec 2021 15:00:06: 20000000 INFO @ Sat, 11 Dec 2021 15:00:09: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:00:17: 17000000 INFO @ Sat, 11 Dec 2021 15:00:18: 21000000 INFO @ Sat, 11 Dec 2021 15:00:21: 25000000 INFO @ Sat, 11 Dec 2021 15:00:29: 22000000 INFO @ Sat, 11 Dec 2021 15:00:29: 18000000 INFO @ Sat, 11 Dec 2021 15:00:32: 26000000 INFO @ Sat, 11 Dec 2021 15:00:40: 23000000 INFO @ Sat, 11 Dec 2021 15:00:41: 19000000 INFO @ Sat, 11 Dec 2021 15:00:44: 27000000 INFO @ Sat, 11 Dec 2021 15:00:52: 24000000 INFO @ Sat, 11 Dec 2021 15:00:53: 20000000 INFO @ Sat, 11 Dec 2021 15:00:55: 28000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:01:03: 25000000 INFO @ Sat, 11 Dec 2021 15:01:05: 21000000 INFO @ Sat, 11 Dec 2021 15:01:07: 29000000 INFO @ Sat, 11 Dec 2021 15:01:15: 26000000 INFO @ Sat, 11 Dec 2021 15:01:17: 22000000 INFO @ Sat, 11 Dec 2021 15:01:18: 30000000 INFO @ Sat, 11 Dec 2021 15:01:26: 27000000 INFO @ Sat, 11 Dec 2021 15:01:29: 23000000 INFO @ Sat, 11 Dec 2021 15:01:30: 31000000 INFO @ Sat, 11 Dec 2021 15:01:38: 28000000 INFO @ Sat, 11 Dec 2021 15:01:41: 32000000 INFO @ Sat, 11 Dec 2021 15:01:42: 24000000 INFO @ Sat, 11 Dec 2021 15:01:49: 29000000 INFO @ Sat, 11 Dec 2021 15:01:53: 33000000 INFO @ Sat, 11 Dec 2021 15:01:54: 25000000 INFO @ Sat, 11 Dec 2021 15:02:01: 30000000 INFO @ Sat, 11 Dec 2021 15:02:04: 34000000 INFO @ Sat, 11 Dec 2021 15:02:06: 26000000 INFO @ Sat, 11 Dec 2021 15:02:12: 31000000 INFO @ Sat, 11 Dec 2021 15:02:16: 35000000 INFO @ Sat, 11 Dec 2021 15:02:18: 27000000 INFO @ Sat, 11 Dec 2021 15:02:24: 32000000 INFO @ Sat, 11 Dec 2021 15:02:28: 36000000 INFO @ Sat, 11 Dec 2021 15:02:30: 28000000 INFO @ Sat, 11 Dec 2021 15:02:36: 33000000 INFO @ Sat, 11 Dec 2021 15:02:39: 37000000 INFO @ Sat, 11 Dec 2021 15:02:42: 29000000 INFO @ Sat, 11 Dec 2021 15:02:47: 34000000 INFO @ Sat, 11 Dec 2021 15:02:51: 38000000 INFO @ Sat, 11 Dec 2021 15:02:54: 30000000 INFO @ Sat, 11 Dec 2021 15:02:59: 35000000 INFO @ Sat, 11 Dec 2021 15:03:02: 39000000 INFO @ Sat, 11 Dec 2021 15:03:06: 31000000 INFO @ Sat, 11 Dec 2021 15:03:10: 36000000 INFO @ Sat, 11 Dec 2021 15:03:14: 40000000 INFO @ Sat, 11 Dec 2021 15:03:18: 32000000 INFO @ Sat, 11 Dec 2021 15:03:22: 37000000 INFO @ Sat, 11 Dec 2021 15:03:25: 41000000 INFO @ Sat, 11 Dec 2021 15:03:29: #1 tag size is determined as 129 bps INFO @ Sat, 11 Dec 2021 15:03:29: #1 tag size = 129 INFO @ Sat, 11 Dec 2021 15:03:29: #1 total tags in treatment: 17639690 INFO @ Sat, 11 Dec 2021 15:03:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:03:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:03:29: #1 tags after filtering in treatment: 11014735 INFO @ Sat, 11 Dec 2021 15:03:29: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:03:29: #1 finished! INFO @ Sat, 11 Dec 2021 15:03:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:03:30: #2 number of paired peaks: 6487 INFO @ Sat, 11 Dec 2021 15:03:30: start model_add_line... INFO @ Sat, 11 Dec 2021 15:03:30: start X-correlation... INFO @ Sat, 11 Dec 2021 15:03:30: end of X-cor INFO @ Sat, 11 Dec 2021 15:03:30: #2 finished! INFO @ Sat, 11 Dec 2021 15:03:30: #2 predicted fragment length is 276 bps INFO @ Sat, 11 Dec 2021 15:03:30: #2 alternative fragment length(s) may be 276 bps INFO @ Sat, 11 Dec 2021 15:03:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.05_model.r INFO @ Sat, 11 Dec 2021 15:03:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:03:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:03:31: 33000000 INFO @ Sat, 11 Dec 2021 15:03:33: 38000000 INFO @ Sat, 11 Dec 2021 15:03:43: 34000000 INFO @ Sat, 11 Dec 2021 15:03:44: 39000000 INFO @ Sat, 11 Dec 2021 15:03:55: 35000000 INFO @ Sat, 11 Dec 2021 15:03:56: 40000000 INFO @ Sat, 11 Dec 2021 15:04:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:04:07: 36000000 INFO @ Sat, 11 Dec 2021 15:04:07: 41000000 INFO @ Sat, 11 Dec 2021 15:04:10: #1 tag size is determined as 129 bps INFO @ Sat, 11 Dec 2021 15:04:10: #1 tag size = 129 INFO @ Sat, 11 Dec 2021 15:04:10: #1 total tags in treatment: 17639690 INFO @ Sat, 11 Dec 2021 15:04:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:04:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:04:10: #1 tags after filtering in treatment: 11014735 INFO @ Sat, 11 Dec 2021 15:04:10: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:04:10: #1 finished! INFO @ Sat, 11 Dec 2021 15:04:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:04:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:04:12: #2 number of paired peaks: 6487 INFO @ Sat, 11 Dec 2021 15:04:12: start model_add_line... INFO @ Sat, 11 Dec 2021 15:04:12: start X-correlation... INFO @ Sat, 11 Dec 2021 15:04:12: end of X-cor INFO @ Sat, 11 Dec 2021 15:04:12: #2 finished! INFO @ Sat, 11 Dec 2021 15:04:12: #2 predicted fragment length is 276 bps INFO @ Sat, 11 Dec 2021 15:04:12: #2 alternative fragment length(s) may be 276 bps INFO @ Sat, 11 Dec 2021 15:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.10_model.r INFO @ Sat, 11 Dec 2021 15:04:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:04:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:04:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:04:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.05_summits.bed INFO @ Sat, 11 Dec 2021 15:04:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7475 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:04:17: 37000000 INFO @ Sat, 11 Dec 2021 15:04:28: 38000000 INFO @ Sat, 11 Dec 2021 15:04:38: 39000000 INFO @ Sat, 11 Dec 2021 15:04:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:04:48: 40000000 INFO @ Sat, 11 Dec 2021 15:04:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:04:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:04:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.10_summits.bed INFO @ Sat, 11 Dec 2021 15:04:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6659 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:04:59: 41000000 INFO @ Sat, 11 Dec 2021 15:05:02: #1 tag size is determined as 129 bps INFO @ Sat, 11 Dec 2021 15:05:02: #1 tag size = 129 INFO @ Sat, 11 Dec 2021 15:05:02: #1 total tags in treatment: 17639690 INFO @ Sat, 11 Dec 2021 15:05:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:05:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:05:02: #1 tags after filtering in treatment: 11014735 INFO @ Sat, 11 Dec 2021 15:05:02: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 11 Dec 2021 15:05:02: #1 finished! INFO @ Sat, 11 Dec 2021 15:05:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:05:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:05:03: #2 number of paired peaks: 6487 INFO @ Sat, 11 Dec 2021 15:05:03: start model_add_line... INFO @ Sat, 11 Dec 2021 15:05:03: start X-correlation... INFO @ Sat, 11 Dec 2021 15:05:03: end of X-cor INFO @ Sat, 11 Dec 2021 15:05:03: #2 finished! INFO @ Sat, 11 Dec 2021 15:05:03: #2 predicted fragment length is 276 bps INFO @ Sat, 11 Dec 2021 15:05:03: #2 alternative fragment length(s) may be 276 bps INFO @ Sat, 11 Dec 2021 15:05:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.20_model.r INFO @ Sat, 11 Dec 2021 15:05:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:05:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:05:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:05:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:05:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:05:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7889139/SRX7889139.20_summits.bed INFO @ Sat, 11 Dec 2021 15:05:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5934 records, 4 fields): 8 millis CompletedMACS2peakCalling