Job ID = 6368762 SRX = SRX5545247 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:34 prefetch.2.10.7: 1) Downloading 'SRR8754491'... 2020-06-16T00:26:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:01 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:01 prefetch.2.10.7: 1) 'SRR8754491' was downloaded successfully 2020-06-16T00:29:01 prefetch.2.10.7: 'SRR8754491' has 0 unresolved dependencies Read 45500660 spots for SRR8754491/SRR8754491.sra Written 45500660 spots for SRR8754491/SRR8754491.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: 00:08:29 45500660 reads; of these: 45500660 (100.00%) were unpaired; of these: 10043719 (22.07%) aligned 0 times 29768155 (65.42%) aligned exactly 1 time 5688786 (12.50%) aligned >1 times 77.93% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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_rmdupse_core] 9706417 / 35456941 = 0.2738 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 09:45:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.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 09:45:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:54: 1000000 INFO @ Tue, 16 Jun 2020 09:45:59: 2000000 INFO @ Tue, 16 Jun 2020 09:46:04: 3000000 INFO @ Tue, 16 Jun 2020 09:46:09: 4000000 INFO @ Tue, 16 Jun 2020 09:46:14: 5000000 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 09:46:19: 6000000 INFO @ Tue, 16 Jun 2020 09:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.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 09:46:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:24: 7000000 INFO @ Tue, 16 Jun 2020 09:46:25: 1000000 INFO @ Tue, 16 Jun 2020 09:46:29: 8000000 INFO @ Tue, 16 Jun 2020 09:46:30: 2000000 INFO @ Tue, 16 Jun 2020 09:46:34: 9000000 INFO @ Tue, 16 Jun 2020 09:46:35: 3000000 INFO @ Tue, 16 Jun 2020 09:46:40: 10000000 INFO @ Tue, 16 Jun 2020 09:46:41: 4000000 INFO @ Tue, 16 Jun 2020 09:46:45: 11000000 INFO @ Tue, 16 Jun 2020 09:46:46: 5000000 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 09:46:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.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 09:46:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:50: 12000000 INFO @ Tue, 16 Jun 2020 09:46:51: 6000000 INFO @ Tue, 16 Jun 2020 09:46:55: 1000000 INFO @ Tue, 16 Jun 2020 09:46:56: 13000000 INFO @ Tue, 16 Jun 2020 09:46:57: 7000000 INFO @ Tue, 16 Jun 2020 09:47:00: 2000000 INFO @ Tue, 16 Jun 2020 09:47:01: 14000000 INFO @ Tue, 16 Jun 2020 09:47:02: 8000000 INFO @ Tue, 16 Jun 2020 09:47:06: 3000000 INFO @ Tue, 16 Jun 2020 09:47:07: 15000000 INFO @ Tue, 16 Jun 2020 09:47:07: 9000000 INFO @ Tue, 16 Jun 2020 09:47:11: 4000000 INFO @ Tue, 16 Jun 2020 09:47:12: 16000000 INFO @ Tue, 16 Jun 2020 09:47:13: 10000000 INFO @ Tue, 16 Jun 2020 09:47:16: 5000000 INFO @ Tue, 16 Jun 2020 09:47:18: 17000000 INFO @ Tue, 16 Jun 2020 09:47:18: 11000000 INFO @ Tue, 16 Jun 2020 09:47:22: 6000000 INFO @ Tue, 16 Jun 2020 09:47:23: 18000000 INFO @ Tue, 16 Jun 2020 09:47:23: 12000000 INFO @ Tue, 16 Jun 2020 09:47:27: 7000000 INFO @ Tue, 16 Jun 2020 09:47:29: 13000000 INFO @ Tue, 16 Jun 2020 09:47:29: 19000000 INFO @ Tue, 16 Jun 2020 09:47:33: 8000000 INFO @ Tue, 16 Jun 2020 09:47:34: 14000000 INFO @ Tue, 16 Jun 2020 09:47:34: 20000000 INFO @ Tue, 16 Jun 2020 09:47:38: 9000000 INFO @ Tue, 16 Jun 2020 09:47:39: 15000000 INFO @ Tue, 16 Jun 2020 09:47:39: 21000000 INFO @ Tue, 16 Jun 2020 09:47:43: 10000000 INFO @ Tue, 16 Jun 2020 09:47:45: 16000000 INFO @ Tue, 16 Jun 2020 09:47:45: 22000000 INFO @ Tue, 16 Jun 2020 09:47:49: 11000000 INFO @ Tue, 16 Jun 2020 09:47:50: 17000000 INFO @ Tue, 16 Jun 2020 09:47:50: 23000000 INFO @ Tue, 16 Jun 2020 09:47:54: 12000000 INFO @ Tue, 16 Jun 2020 09:47:55: 18000000 INFO @ Tue, 16 Jun 2020 09:47:56: 24000000 INFO @ Tue, 16 Jun 2020 09:48:00: 13000000 INFO @ Tue, 16 Jun 2020 09:48:01: 19000000 INFO @ Tue, 16 Jun 2020 09:48:01: 25000000 INFO @ Tue, 16 Jun 2020 09:48:05: 14000000 INFO @ Tue, 16 Jun 2020 09:48:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:05: #1 total tags in treatment: 25750524 INFO @ Tue, 16 Jun 2020 09:48:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:05: #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 09:48:06: #1 tags after filtering in treatment: 25750524 INFO @ Tue, 16 Jun 2020 09:48:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:06: 20000000 INFO @ Tue, 16 Jun 2020 09:48:07: #2 number of paired peaks: 126 WARNING @ Tue, 16 Jun 2020 09:48:07: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:07: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:48:07: #2 alternative fragment length(s) may be 1,49,541 bps INFO @ Tue, 16 Jun 2020 09:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:07: #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 09:48:07: #2 You may need to consider one of the other alternative d(s): 1,49,541 WARNING @ Tue, 16 Jun 2020 09:48:07: #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 09:48:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:10: 15000000 INFO @ Tue, 16 Jun 2020 09:48:11: 21000000 INFO @ Tue, 16 Jun 2020 09:48:16: 16000000 INFO @ Tue, 16 Jun 2020 09:48:17: 22000000 INFO @ Tue, 16 Jun 2020 09:48:21: 17000000 INFO @ Tue, 16 Jun 2020 09:48:22: 23000000 INFO @ Tue, 16 Jun 2020 09:48:26: 18000000 INFO @ Tue, 16 Jun 2020 09:48:27: 24000000 INFO @ Tue, 16 Jun 2020 09:48:32: 19000000 INFO @ Tue, 16 Jun 2020 09:48:33: 25000000 INFO @ Tue, 16 Jun 2020 09:48:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:37: #1 total tags in treatment: 25750524 INFO @ Tue, 16 Jun 2020 09:48:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:37: #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 09:48:37: 20000000 INFO @ Tue, 16 Jun 2020 09:48:37: #1 tags after filtering in treatment: 25750524 INFO @ Tue, 16 Jun 2020 09:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:37: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:39: #2 number of paired peaks: 126 WARNING @ Tue, 16 Jun 2020 09:48:39: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:48:39: #2 alternative fragment length(s) may be 1,49,541 bps INFO @ Tue, 16 Jun 2020 09:48:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:39: #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 09:48:39: #2 You may need to consider one of the other alternative d(s): 1,49,541 WARNING @ Tue, 16 Jun 2020 09:48:39: #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 09:48:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:42: 21000000 INFO @ Tue, 16 Jun 2020 09:48:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:47: 22000000 INFO @ Tue, 16 Jun 2020 09:48:52: 23000000 INFO @ Tue, 16 Jun 2020 09:48:57: 24000000 INFO @ Tue, 16 Jun 2020 09:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:02: 25000000 INFO @ Tue, 16 Jun 2020 09:49:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:06: #1 total tags in treatment: 25750524 INFO @ Tue, 16 Jun 2020 09:49:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:06: #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 09:49:07: #1 tags after filtering in treatment: 25750524 INFO @ Tue, 16 Jun 2020 09:49:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:08: #2 number of paired peaks: 126 WARNING @ Tue, 16 Jun 2020 09:49:08: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:08: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:49:08: #2 alternative fragment length(s) may be 1,49,541 bps INFO @ Tue, 16 Jun 2020 09:49:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:08: #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 09:49:08: #2 You may need to consider one of the other alternative d(s): 1,49,541 WARNING @ Tue, 16 Jun 2020 09:49:08: #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 09:49:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:33: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5545247/SRX5545247.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling