Job ID = 14158499 SRX = SRX8976702 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16433460 spots for SRR12483306/SRR12483306.sra Written 16433460 spots for SRR12483306/SRR12483306.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159143 ("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: 00:13:26 16433460 reads; of these: 16433460 (100.00%) were paired; of these: 1439853 (8.76%) aligned concordantly 0 times 12986202 (79.02%) aligned concordantly exactly 1 time 2007405 (12.22%) aligned concordantly >1 times ---- 1439853 pairs aligned concordantly 0 times; of these: 972304 (67.53%) aligned discordantly 1 time ---- 467549 pairs aligned 0 times concordantly or discordantly; of these: 935098 mates make up the pairs; of these: 372309 (39.81%) aligned 0 times 297473 (31.81%) aligned exactly 1 time 265316 (28.37%) aligned >1 times 98.87% overall alignment rate Time searching: 00:13:26 Overall time: 00:13:26 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 16 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] 278436 / 15944101 = 0.0175 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 17:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.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 17:59:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:59:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:59:57: 1000000 INFO @ Wed, 08 Dec 2021 18:00:02: 2000000 INFO @ Wed, 08 Dec 2021 18:00:08: 3000000 INFO @ Wed, 08 Dec 2021 18:00:13: 4000000 INFO @ Wed, 08 Dec 2021 18:00:19: 5000000 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 18:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.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 18:00:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:00:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:00:25: 6000000 INFO @ Wed, 08 Dec 2021 18:00:26: 1000000 INFO @ Wed, 08 Dec 2021 18:00:31: 7000000 INFO @ Wed, 08 Dec 2021 18:00:31: 2000000 INFO @ Wed, 08 Dec 2021 18:00:36: 3000000 INFO @ Wed, 08 Dec 2021 18:00:37: 8000000 INFO @ Wed, 08 Dec 2021 18:00:41: 4000000 INFO @ Wed, 08 Dec 2021 18:00:43: 9000000 INFO @ Wed, 08 Dec 2021 18:00:46: 5000000 INFO @ Wed, 08 Dec 2021 18:00:49: 10000000 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 18:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.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 18:00:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:00:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:00:52: 6000000 INFO @ Wed, 08 Dec 2021 18:00:55: 11000000 INFO @ Wed, 08 Dec 2021 18:00:56: 1000000 INFO @ Wed, 08 Dec 2021 18:00:57: 7000000 INFO @ Wed, 08 Dec 2021 18:01:01: 12000000 INFO @ Wed, 08 Dec 2021 18:01:01: 2000000 INFO @ Wed, 08 Dec 2021 18:01:02: 8000000 INFO @ Wed, 08 Dec 2021 18:01:06: 3000000 INFO @ Wed, 08 Dec 2021 18:01:07: 13000000 INFO @ Wed, 08 Dec 2021 18:01:07: 9000000 INFO @ Wed, 08 Dec 2021 18:01:11: 4000000 INFO @ Wed, 08 Dec 2021 18:01:12: 10000000 INFO @ Wed, 08 Dec 2021 18:01:13: 14000000 INFO @ Wed, 08 Dec 2021 18:01:16: 5000000 INFO @ Wed, 08 Dec 2021 18:01:17: 11000000 INFO @ Wed, 08 Dec 2021 18:01:19: 15000000 INFO @ Wed, 08 Dec 2021 18:01:22: 6000000 INFO @ Wed, 08 Dec 2021 18:01:22: 12000000 INFO @ Wed, 08 Dec 2021 18:01:25: 16000000 INFO @ Wed, 08 Dec 2021 18:01:27: 7000000 INFO @ Wed, 08 Dec 2021 18:01:27: 13000000 INFO @ Wed, 08 Dec 2021 18:01:31: 17000000 INFO @ Wed, 08 Dec 2021 18:01:32: 8000000 INFO @ Wed, 08 Dec 2021 18:01:32: 14000000 INFO @ Wed, 08 Dec 2021 18:01:37: 18000000 INFO @ Wed, 08 Dec 2021 18:01:37: 9000000 INFO @ Wed, 08 Dec 2021 18:01:37: 15000000 INFO @ Wed, 08 Dec 2021 18:01:42: 10000000 INFO @ Wed, 08 Dec 2021 18:01:43: 19000000 INFO @ Wed, 08 Dec 2021 18:01:43: 16000000 INFO @ Wed, 08 Dec 2021 18:01:47: 11000000 INFO @ Wed, 08 Dec 2021 18:01:48: 17000000 INFO @ Wed, 08 Dec 2021 18:01:48: 20000000 INFO @ Wed, 08 Dec 2021 18:01:52: 12000000 INFO @ Wed, 08 Dec 2021 18:01:53: 18000000 INFO @ Wed, 08 Dec 2021 18:01:54: 21000000 INFO @ Wed, 08 Dec 2021 18:01:57: 13000000 INFO @ Wed, 08 Dec 2021 18:01:58: 19000000 INFO @ Wed, 08 Dec 2021 18:02:00: 22000000 INFO @ Wed, 08 Dec 2021 18:02:02: 14000000 INFO @ Wed, 08 Dec 2021 18:02:03: 20000000 INFO @ Wed, 08 Dec 2021 18:02:06: 23000000 INFO @ Wed, 08 Dec 2021 18:02:07: 15000000 INFO @ Wed, 08 Dec 2021 18:02:08: 21000000 INFO @ Wed, 08 Dec 2021 18:02:12: 16000000 INFO @ Wed, 08 Dec 2021 18:02:12: 24000000 INFO @ Wed, 08 Dec 2021 18:02:13: 22000000 INFO @ Wed, 08 Dec 2021 18:02:17: 17000000 INFO @ Wed, 08 Dec 2021 18:02:18: 25000000 INFO @ Wed, 08 Dec 2021 18:02:19: 23000000 INFO @ Wed, 08 Dec 2021 18:02:22: 18000000 INFO @ Wed, 08 Dec 2021 18:02:24: 24000000 INFO @ Wed, 08 Dec 2021 18:02:24: 26000000 INFO @ Wed, 08 Dec 2021 18:02:27: 19000000 INFO @ Wed, 08 Dec 2021 18:02:29: 25000000 INFO @ Wed, 08 Dec 2021 18:02:30: 27000000 INFO @ Wed, 08 Dec 2021 18:02:32: 20000000 INFO @ Wed, 08 Dec 2021 18:02:34: 26000000 INFO @ Wed, 08 Dec 2021 18:02:36: 28000000 INFO @ Wed, 08 Dec 2021 18:02:37: 21000000 INFO @ Wed, 08 Dec 2021 18:02:39: 27000000 INFO @ Wed, 08 Dec 2021 18:02:42: 29000000 INFO @ Wed, 08 Dec 2021 18:02:42: 22000000 INFO @ Wed, 08 Dec 2021 18:02:44: 28000000 INFO @ Wed, 08 Dec 2021 18:02:47: 23000000 INFO @ Wed, 08 Dec 2021 18:02:48: 30000000 INFO @ Wed, 08 Dec 2021 18:02:49: 29000000 INFO @ Wed, 08 Dec 2021 18:02:52: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:02:54: 30000000 INFO @ Wed, 08 Dec 2021 18:02:54: 31000000 INFO @ Wed, 08 Dec 2021 18:02:58: 25000000 INFO @ Wed, 08 Dec 2021 18:02:59: 31000000 INFO @ Wed, 08 Dec 2021 18:03:00: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:03:00: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:03:00: #1 total tags in treatment: 14725852 INFO @ Wed, 08 Dec 2021 18:03:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:03:00: #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 18:03:00: #1 tags after filtering in treatment: 13626703 INFO @ Wed, 08 Dec 2021 18:03:00: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:03:00: #1 finished! INFO @ Wed, 08 Dec 2021 18:03:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:03:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:03:01: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 18:03:01: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 08 Dec 2021 18:03:01: start model_add_line... INFO @ Wed, 08 Dec 2021 18:03:01: start X-correlation... INFO @ Wed, 08 Dec 2021 18:03:01: end of X-cor INFO @ Wed, 08 Dec 2021 18:03:01: #2 finished! INFO @ Wed, 08 Dec 2021 18:03:01: #2 predicted fragment length is 148 bps INFO @ Wed, 08 Dec 2021 18:03:01: #2 alternative fragment length(s) may be 4,148 bps INFO @ Wed, 08 Dec 2021 18:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.05_model.r INFO @ Wed, 08 Dec 2021 18:03:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:03:02: 26000000 INFO @ Wed, 08 Dec 2021 18:03:04: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:03:04: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:03:04: #1 total tags in treatment: 14725852 INFO @ Wed, 08 Dec 2021 18:03:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:03:04: #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 18:03:04: #1 tags after filtering in treatment: 13626703 INFO @ Wed, 08 Dec 2021 18:03:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:03:04: #1 finished! INFO @ Wed, 08 Dec 2021 18:03:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:03:05: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 18:03:05: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 08 Dec 2021 18:03:05: start model_add_line... INFO @ Wed, 08 Dec 2021 18:03:05: start X-correlation... INFO @ Wed, 08 Dec 2021 18:03:05: end of X-cor INFO @ Wed, 08 Dec 2021 18:03:05: #2 finished! INFO @ Wed, 08 Dec 2021 18:03:05: #2 predicted fragment length is 148 bps INFO @ Wed, 08 Dec 2021 18:03:05: #2 alternative fragment length(s) may be 4,148 bps INFO @ Wed, 08 Dec 2021 18:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.10_model.r INFO @ Wed, 08 Dec 2021 18:03:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:03:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:03:07: 27000000 INFO @ Wed, 08 Dec 2021 18:03:12: 28000000 INFO @ Wed, 08 Dec 2021 18:03:17: 29000000 INFO @ Wed, 08 Dec 2021 18:03:21: 30000000 INFO @ Wed, 08 Dec 2021 18:03:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:03:26: 31000000 INFO @ Wed, 08 Dec 2021 18:03:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:03:31: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:03:31: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:03:31: #1 total tags in treatment: 14725852 INFO @ Wed, 08 Dec 2021 18:03:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:03:31: #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 18:03:31: #1 tags after filtering in treatment: 13626703 INFO @ Wed, 08 Dec 2021 18:03:31: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:03:31: #1 finished! INFO @ Wed, 08 Dec 2021 18:03:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:03:32: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 18:03:32: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 08 Dec 2021 18:03:32: start model_add_line... INFO @ Wed, 08 Dec 2021 18:03:32: start X-correlation... INFO @ Wed, 08 Dec 2021 18:03:32: end of X-cor INFO @ Wed, 08 Dec 2021 18:03:32: #2 finished! INFO @ Wed, 08 Dec 2021 18:03:32: #2 predicted fragment length is 148 bps INFO @ Wed, 08 Dec 2021 18:03:32: #2 alternative fragment length(s) may be 4,148 bps INFO @ Wed, 08 Dec 2021 18:03:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.20_model.r INFO @ Wed, 08 Dec 2021 18:03:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:03:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:03:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:03:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:03:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.05_summits.bed INFO @ Wed, 08 Dec 2021 18:03:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (385 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.10_summits.bed INFO @ Wed, 08 Dec 2021 18:03:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:03:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976702/SRX8976702.20_summits.bed INFO @ Wed, 08 Dec 2021 18:04:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling