Job ID = 14159381 SRX = SRX8976689 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14573006 spots for SRR12483293/SRR12483293.sra Written 14573006 spots for SRR12483293/SRR12483293.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159607 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:00 14573006 reads; of these: 14573006 (100.00%) were paired; of these: 1808987 (12.41%) aligned concordantly 0 times 9339725 (64.09%) aligned concordantly exactly 1 time 3424294 (23.50%) aligned concordantly >1 times ---- 1808987 pairs aligned concordantly 0 times; of these: 1057694 (58.47%) aligned discordantly 1 time ---- 751293 pairs aligned 0 times concordantly or discordantly; of these: 1502586 mates make up the pairs; of these: 416120 (27.69%) aligned 0 times 349430 (23.26%) aligned exactly 1 time 737036 (49.05%) aligned >1 times 98.57% overall alignment rate Time searching: 00:14:00 Overall time: 00:14:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1074685 / 13811143 = 0.0778 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 @ Wed, 08 Dec 2021 21:44:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 21:44:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:44:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:44:27: 1000000 INFO @ Wed, 08 Dec 2021 21:44:33: 2000000 INFO @ Wed, 08 Dec 2021 21:44:39: 3000000 INFO @ Wed, 08 Dec 2021 21:44:44: 4000000 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 @ Wed, 08 Dec 2021 21:44:50: 5000000 INFO @ Wed, 08 Dec 2021 21:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 21:44:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:44:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:44:56: 6000000 INFO @ Wed, 08 Dec 2021 21:44:57: 1000000 INFO @ Wed, 08 Dec 2021 21:45:02: 7000000 INFO @ Wed, 08 Dec 2021 21:45:03: 2000000 INFO @ Wed, 08 Dec 2021 21:45:08: 8000000 INFO @ Wed, 08 Dec 2021 21:45:08: 3000000 INFO @ Wed, 08 Dec 2021 21:45:14: 4000000 INFO @ Wed, 08 Dec 2021 21:45:14: 9000000 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 @ Wed, 08 Dec 2021 21:45:19: 5000000 INFO @ Wed, 08 Dec 2021 21:45:20: 10000000 INFO @ Wed, 08 Dec 2021 21:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Wed, 08 Dec 2021 21:45:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:45:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:45:25: 6000000 INFO @ Wed, 08 Dec 2021 21:45:27: 11000000 INFO @ Wed, 08 Dec 2021 21:45:28: 1000000 INFO @ Wed, 08 Dec 2021 21:45:31: 7000000 INFO @ Wed, 08 Dec 2021 21:45:33: 12000000 INFO @ Wed, 08 Dec 2021 21:45:34: 2000000 INFO @ Wed, 08 Dec 2021 21:45:37: 8000000 INFO @ Wed, 08 Dec 2021 21:45:39: 13000000 INFO @ Wed, 08 Dec 2021 21:45:41: 3000000 INFO @ Wed, 08 Dec 2021 21:45:42: 9000000 INFO @ Wed, 08 Dec 2021 21:45:45: 14000000 INFO @ Wed, 08 Dec 2021 21:45:48: 4000000 INFO @ Wed, 08 Dec 2021 21:45:48: 10000000 INFO @ Wed, 08 Dec 2021 21:45:51: 15000000 INFO @ Wed, 08 Dec 2021 21:45:54: 11000000 INFO @ Wed, 08 Dec 2021 21:45:54: 5000000 INFO @ Wed, 08 Dec 2021 21:45:58: 16000000 INFO @ Wed, 08 Dec 2021 21:46:00: 12000000 INFO @ Wed, 08 Dec 2021 21:46:00: 6000000 INFO @ Wed, 08 Dec 2021 21:46:03: 17000000 INFO @ Wed, 08 Dec 2021 21:46:06: 13000000 INFO @ Wed, 08 Dec 2021 21:46:07: 7000000 INFO @ Wed, 08 Dec 2021 21:46:09: 18000000 INFO @ Wed, 08 Dec 2021 21:46:11: 14000000 INFO @ Wed, 08 Dec 2021 21:46:14: 8000000 INFO @ Wed, 08 Dec 2021 21:46:15: 19000000 INFO @ Wed, 08 Dec 2021 21:46:17: 15000000 INFO @ Wed, 08 Dec 2021 21:46:20: 20000000 INFO @ Wed, 08 Dec 2021 21:46:20: 9000000 INFO @ Wed, 08 Dec 2021 21:46:22: 16000000 INFO @ Wed, 08 Dec 2021 21:46:26: 21000000 INFO @ Wed, 08 Dec 2021 21:46:27: 10000000 INFO @ Wed, 08 Dec 2021 21:46:28: 17000000 INFO @ Wed, 08 Dec 2021 21:46:32: 22000000 INFO @ Wed, 08 Dec 2021 21:46:33: 11000000 INFO @ Wed, 08 Dec 2021 21:46:34: 18000000 INFO @ Wed, 08 Dec 2021 21:46:37: 23000000 INFO @ Wed, 08 Dec 2021 21:46:39: 19000000 INFO @ Wed, 08 Dec 2021 21:46:40: 12000000 INFO @ Wed, 08 Dec 2021 21:46:44: 24000000 INFO @ Wed, 08 Dec 2021 21:46:45: 20000000 INFO @ Wed, 08 Dec 2021 21:46:46: 13000000 INFO @ Wed, 08 Dec 2021 21:46:50: 25000000 INFO @ Wed, 08 Dec 2021 21:46:51: 21000000 INFO @ Wed, 08 Dec 2021 21:46:53: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:46:56: 22000000 INFO @ Wed, 08 Dec 2021 21:46:57: 26000000 INFO @ Wed, 08 Dec 2021 21:47:00: 15000000 INFO @ Wed, 08 Dec 2021 21:47:01: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:47:01: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:47:01: #1 total tags in treatment: 11744700 INFO @ Wed, 08 Dec 2021 21:47:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:47:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:47:01: #1 tags after filtering in treatment: 9539106 INFO @ Wed, 08 Dec 2021 21:47:01: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 21:47:01: #1 finished! INFO @ Wed, 08 Dec 2021 21:47:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:47:02: #2 number of paired peaks: 3907 INFO @ Wed, 08 Dec 2021 21:47:02: start model_add_line... INFO @ Wed, 08 Dec 2021 21:47:02: 23000000 INFO @ Wed, 08 Dec 2021 21:47:02: start X-correlation... INFO @ Wed, 08 Dec 2021 21:47:02: end of X-cor INFO @ Wed, 08 Dec 2021 21:47:02: #2 finished! INFO @ Wed, 08 Dec 2021 21:47:02: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 21:47:02: #2 alternative fragment length(s) may be 2,257 bps INFO @ Wed, 08 Dec 2021 21:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.05_model.r INFO @ Wed, 08 Dec 2021 21:47:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:47:06: 16000000 INFO @ Wed, 08 Dec 2021 21:47:08: 24000000 INFO @ Wed, 08 Dec 2021 21:47:13: 17000000 INFO @ Wed, 08 Dec 2021 21:47:13: 25000000 INFO @ Wed, 08 Dec 2021 21:47:19: 26000000 INFO @ Wed, 08 Dec 2021 21:47:19: 18000000 INFO @ Wed, 08 Dec 2021 21:47:22: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:47:22: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:47:22: #1 total tags in treatment: 11744700 INFO @ Wed, 08 Dec 2021 21:47:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:47:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:47:23: #1 tags after filtering in treatment: 9539106 INFO @ Wed, 08 Dec 2021 21:47:23: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 21:47:23: #1 finished! INFO @ Wed, 08 Dec 2021 21:47:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:47:23: #2 number of paired peaks: 3907 INFO @ Wed, 08 Dec 2021 21:47:23: start model_add_line... INFO @ Wed, 08 Dec 2021 21:47:24: start X-correlation... INFO @ Wed, 08 Dec 2021 21:47:24: end of X-cor INFO @ Wed, 08 Dec 2021 21:47:24: #2 finished! INFO @ Wed, 08 Dec 2021 21:47:24: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 21:47:24: #2 alternative fragment length(s) may be 2,257 bps INFO @ Wed, 08 Dec 2021 21:47:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.10_model.r INFO @ Wed, 08 Dec 2021 21:47:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:47:26: 19000000 INFO @ Wed, 08 Dec 2021 21:47:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:47:32: 20000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:47:38: 21000000 INFO @ Wed, 08 Dec 2021 21:47:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:47:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:47:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.05_summits.bed INFO @ Wed, 08 Dec 2021 21:47:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1721 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:47:44: 22000000 INFO @ Wed, 08 Dec 2021 21:47:50: 23000000 INFO @ Wed, 08 Dec 2021 21:47:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:47:56: 24000000 INFO @ Wed, 08 Dec 2021 21:48:02: 25000000 INFO @ Wed, 08 Dec 2021 21:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.10_summits.bed INFO @ Wed, 08 Dec 2021 21:48:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:48:08: 26000000 INFO @ Wed, 08 Dec 2021 21:48:11: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:48:11: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:48:11: #1 total tags in treatment: 11744700 INFO @ Wed, 08 Dec 2021 21:48:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:48:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:48:11: #1 tags after filtering in treatment: 9539106 INFO @ Wed, 08 Dec 2021 21:48:11: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 21:48:11: #1 finished! INFO @ Wed, 08 Dec 2021 21:48:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:48:12: #2 number of paired peaks: 3907 INFO @ Wed, 08 Dec 2021 21:48:12: start model_add_line... INFO @ Wed, 08 Dec 2021 21:48:12: start X-correlation... INFO @ Wed, 08 Dec 2021 21:48:12: end of X-cor INFO @ Wed, 08 Dec 2021 21:48:12: #2 finished! INFO @ Wed, 08 Dec 2021 21:48:12: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 21:48:12: #2 alternative fragment length(s) may be 2,257 bps INFO @ Wed, 08 Dec 2021 21:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.20_model.r INFO @ Wed, 08 Dec 2021 21:48:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:48:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976689/SRX8976689.20_summits.bed INFO @ Wed, 08 Dec 2021 21:48:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (302 records, 4 fields): 1 millis CompletedMACS2peakCalling