Job ID = 6366521 SRX = SRX1674101 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:56 prefetch.2.10.7: 1) Downloading 'SRR3320147'... 2020-06-15T22:51:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:02 prefetch.2.10.7: 1) 'SRR3320147' was downloaded successfully Read 58288493 spots for SRR3320147/SRR3320147.sra Written 58288493 spots for SRR3320147/SRR3320147.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:52 58288493 reads; of these: 58288493 (100.00%) were unpaired; of these: 1868901 (3.21%) aligned 0 times 50299292 (86.29%) aligned exactly 1 time 6120300 (10.50%) aligned >1 times 96.79% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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 24 files... [bam_rmdupse_core] 23735474 / 56419592 = 0.4207 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.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 @ Tue, 16 Jun 2020 08:23:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:09: 1000000 INFO @ Tue, 16 Jun 2020 08:23:15: 2000000 INFO @ Tue, 16 Jun 2020 08:23:21: 3000000 INFO @ Tue, 16 Jun 2020 08:23:27: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:23:33: 5000000 INFO @ Tue, 16 Jun 2020 08:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.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 @ Tue, 16 Jun 2020 08:23:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:23:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:23:39: 6000000 INFO @ Tue, 16 Jun 2020 08:23:39: 1000000 INFO @ Tue, 16 Jun 2020 08:23:46: 7000000 INFO @ Tue, 16 Jun 2020 08:23:46: 2000000 INFO @ Tue, 16 Jun 2020 08:23:52: 3000000 INFO @ Tue, 16 Jun 2020 08:23:52: 8000000 INFO @ Tue, 16 Jun 2020 08:23:59: 4000000 INFO @ Tue, 16 Jun 2020 08:23:59: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.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 @ Tue, 16 Jun 2020 08:24:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:05: 5000000 INFO @ Tue, 16 Jun 2020 08:24:06: 10000000 INFO @ Tue, 16 Jun 2020 08:24:11: 1000000 INFO @ Tue, 16 Jun 2020 08:24:12: 6000000 INFO @ Tue, 16 Jun 2020 08:24:13: 11000000 INFO @ Tue, 16 Jun 2020 08:24:20: 2000000 INFO @ Tue, 16 Jun 2020 08:24:20: 7000000 INFO @ Tue, 16 Jun 2020 08:24:20: 12000000 INFO @ Tue, 16 Jun 2020 08:24:27: 8000000 INFO @ Tue, 16 Jun 2020 08:24:28: 3000000 INFO @ Tue, 16 Jun 2020 08:24:28: 13000000 INFO @ Tue, 16 Jun 2020 08:24:35: 9000000 INFO @ Tue, 16 Jun 2020 08:24:35: 14000000 INFO @ Tue, 16 Jun 2020 08:24:36: 4000000 INFO @ Tue, 16 Jun 2020 08:24:42: 10000000 INFO @ Tue, 16 Jun 2020 08:24:43: 15000000 INFO @ Tue, 16 Jun 2020 08:24:44: 5000000 INFO @ Tue, 16 Jun 2020 08:24:49: 11000000 INFO @ Tue, 16 Jun 2020 08:24:50: 16000000 INFO @ Tue, 16 Jun 2020 08:24:52: 6000000 INFO @ Tue, 16 Jun 2020 08:24:57: 12000000 INFO @ Tue, 16 Jun 2020 08:24:57: 17000000 INFO @ Tue, 16 Jun 2020 08:25:00: 7000000 INFO @ Tue, 16 Jun 2020 08:25:04: 13000000 INFO @ Tue, 16 Jun 2020 08:25:05: 18000000 INFO @ Tue, 16 Jun 2020 08:25:08: 8000000 INFO @ Tue, 16 Jun 2020 08:25:11: 14000000 INFO @ Tue, 16 Jun 2020 08:25:12: 19000000 INFO @ Tue, 16 Jun 2020 08:25:16: 9000000 INFO @ Tue, 16 Jun 2020 08:25:19: 15000000 INFO @ Tue, 16 Jun 2020 08:25:20: 20000000 INFO @ Tue, 16 Jun 2020 08:25:24: 10000000 INFO @ Tue, 16 Jun 2020 08:25:26: 16000000 INFO @ Tue, 16 Jun 2020 08:25:27: 21000000 INFO @ Tue, 16 Jun 2020 08:25:33: 11000000 INFO @ Tue, 16 Jun 2020 08:25:33: 17000000 INFO @ Tue, 16 Jun 2020 08:25:34: 22000000 INFO @ Tue, 16 Jun 2020 08:25:41: 18000000 INFO @ Tue, 16 Jun 2020 08:25:41: 12000000 INFO @ Tue, 16 Jun 2020 08:25:42: 23000000 INFO @ Tue, 16 Jun 2020 08:25:48: 19000000 INFO @ Tue, 16 Jun 2020 08:25:49: 24000000 INFO @ Tue, 16 Jun 2020 08:25:50: 13000000 INFO @ Tue, 16 Jun 2020 08:25:56: 20000000 INFO @ Tue, 16 Jun 2020 08:25:57: 25000000 INFO @ Tue, 16 Jun 2020 08:25:58: 14000000 INFO @ Tue, 16 Jun 2020 08:26:03: 21000000 INFO @ Tue, 16 Jun 2020 08:26:04: 26000000 INFO @ Tue, 16 Jun 2020 08:26:06: 15000000 INFO @ Tue, 16 Jun 2020 08:26:11: 22000000 INFO @ Tue, 16 Jun 2020 08:26:11: 27000000 INFO @ Tue, 16 Jun 2020 08:26:15: 16000000 INFO @ Tue, 16 Jun 2020 08:26:18: 23000000 INFO @ Tue, 16 Jun 2020 08:26:19: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:24: 17000000 INFO @ Tue, 16 Jun 2020 08:26:25: 24000000 INFO @ Tue, 16 Jun 2020 08:26:26: 29000000 INFO @ Tue, 16 Jun 2020 08:26:32: 18000000 INFO @ Tue, 16 Jun 2020 08:26:33: 25000000 INFO @ Tue, 16 Jun 2020 08:26:33: 30000000 INFO @ Tue, 16 Jun 2020 08:26:40: 26000000 INFO @ Tue, 16 Jun 2020 08:26:41: 19000000 INFO @ Tue, 16 Jun 2020 08:26:41: 31000000 INFO @ Tue, 16 Jun 2020 08:26:47: 27000000 INFO @ Tue, 16 Jun 2020 08:26:48: 32000000 INFO @ Tue, 16 Jun 2020 08:26:49: 20000000 INFO @ Tue, 16 Jun 2020 08:26:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:53: #1 total tags in treatment: 32684118 INFO @ Tue, 16 Jun 2020 08:26:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:26:54: #1 tags after filtering in treatment: 32684118 INFO @ Tue, 16 Jun 2020 08:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:54: 28000000 INFO @ Tue, 16 Jun 2020 08:26:56: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 08:26:56: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:26:56: #2 alternative fragment length(s) may be 1,39,78,98,123,152,178,205,235 bps INFO @ Tue, 16 Jun 2020 08:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:56: #2 You may need to consider one of the other alternative d(s): 1,39,78,98,123,152,178,205,235 WARNING @ Tue, 16 Jun 2020 08:26:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:26:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:57: 21000000 INFO @ Tue, 16 Jun 2020 08:27:01: 29000000 INFO @ Tue, 16 Jun 2020 08:27:05: 22000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:27:08: 30000000 INFO @ Tue, 16 Jun 2020 08:27:14: 23000000 INFO @ Tue, 16 Jun 2020 08:27:15: 31000000 INFO @ Tue, 16 Jun 2020 08:27:22: 24000000 INFO @ Tue, 16 Jun 2020 08:27:22: 32000000 INFO @ Tue, 16 Jun 2020 08:27:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:27: #1 total tags in treatment: 32684118 INFO @ Tue, 16 Jun 2020 08:27:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:27:28: #1 tags after filtering in treatment: 32684118 INFO @ Tue, 16 Jun 2020 08:27:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:30: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 08:27:30: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:30: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:27:30: #2 alternative fragment length(s) may be 1,39,78,98,123,152,178,205,235 bps INFO @ Tue, 16 Jun 2020 08:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.10_model.r WARNING @ Tue, 16 Jun 2020 08:27:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:30: #2 You may need to consider one of the other alternative d(s): 1,39,78,98,123,152,178,205,235 WARNING @ Tue, 16 Jun 2020 08:27:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:27:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:30: 25000000 INFO @ Tue, 16 Jun 2020 08:27:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:38: 26000000 INFO @ Tue, 16 Jun 2020 08:27:45: 27000000 INFO @ Tue, 16 Jun 2020 08:27:52: 28000000 INFO @ Tue, 16 Jun 2020 08:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:00: 29000000 INFO @ Tue, 16 Jun 2020 08:28:07: 30000000 INFO @ Tue, 16 Jun 2020 08:28:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:15: 31000000 INFO @ Tue, 16 Jun 2020 08:28:22: 32000000 INFO @ Tue, 16 Jun 2020 08:28:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:28:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:28:27: #1 total tags in treatment: 32684118 INFO @ Tue, 16 Jun 2020 08:28:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:28:28: #1 tags after filtering in treatment: 32684118 INFO @ Tue, 16 Jun 2020 08:28:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:30: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 08:28:30: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:30: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:28:30: #2 alternative fragment length(s) may be 1,39,78,98,123,152,178,205,235 bps INFO @ Tue, 16 Jun 2020 08:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:30: #2 You may need to consider one of the other alternative d(s): 1,39,78,98,123,152,178,205,235 WARNING @ Tue, 16 Jun 2020 08:28:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674101/SRX1674101.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling