Job ID = 6366526 SRX = SRX172527 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:55:14 prefetch.2.10.7: 1) Downloading 'SRR530782'... 2020-06-15T22:55:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:21 prefetch.2.10.7: 1) 'SRR530782' was downloaded successfully Read 23992486 spots for SRR530782/SRR530782.sra Written 23992486 spots for SRR530782/SRR530782.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: 00:05:32 23992486 reads; of these: 23992486 (100.00%) were unpaired; of these: 2093303 (8.72%) aligned 0 times 17555635 (73.17%) aligned exactly 1 time 4343548 (18.10%) aligned >1 times 91.28% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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_rmdupse_core] 7736049 / 21899183 = 0.3533 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 08:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.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 08:09:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:17: 1000000 INFO @ Tue, 16 Jun 2020 08:09:22: 2000000 INFO @ Tue, 16 Jun 2020 08:09:27: 3000000 INFO @ Tue, 16 Jun 2020 08:09:32: 4000000 INFO @ Tue, 16 Jun 2020 08:09:37: 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 08:09:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.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 08:09:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:42: 6000000 INFO @ Tue, 16 Jun 2020 08:09:47: 1000000 INFO @ Tue, 16 Jun 2020 08:09:48: 7000000 INFO @ Tue, 16 Jun 2020 08:09:52: 2000000 INFO @ Tue, 16 Jun 2020 08:09:53: 8000000 INFO @ Tue, 16 Jun 2020 08:09:58: 3000000 INFO @ Tue, 16 Jun 2020 08:09:59: 9000000 INFO @ Tue, 16 Jun 2020 08:10:03: 4000000 INFO @ Tue, 16 Jun 2020 08:10:04: 10000000 INFO @ Tue, 16 Jun 2020 08:10:08: 5000000 INFO @ Tue, 16 Jun 2020 08:10:09: 11000000 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 08:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.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 08:10:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:14: 6000000 INFO @ Tue, 16 Jun 2020 08:10:15: 12000000 INFO @ Tue, 16 Jun 2020 08:10:18: 1000000 INFO @ Tue, 16 Jun 2020 08:10:19: 7000000 INFO @ Tue, 16 Jun 2020 08:10:20: 13000000 INFO @ Tue, 16 Jun 2020 08:10:23: 2000000 INFO @ Tue, 16 Jun 2020 08:10:25: 8000000 INFO @ Tue, 16 Jun 2020 08:10:26: 14000000 INFO @ Tue, 16 Jun 2020 08:10:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:27: #1 total tags in treatment: 14163134 INFO @ Tue, 16 Jun 2020 08:10:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:27: #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 08:10:27: #1 tags after filtering in treatment: 14163134 INFO @ Tue, 16 Jun 2020 08:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:28: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:10:28: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:28: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:10:28: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 16 Jun 2020 08:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:28: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:28: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 16 Jun 2020 08:10:28: #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 08:10:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:28: 3000000 INFO @ Tue, 16 Jun 2020 08:10:30: 9000000 INFO @ Tue, 16 Jun 2020 08:10:34: 4000000 INFO @ Tue, 16 Jun 2020 08:10:36: 10000000 INFO @ Tue, 16 Jun 2020 08:10:39: 5000000 INFO @ Tue, 16 Jun 2020 08:10:41: 11000000 INFO @ Tue, 16 Jun 2020 08:10:45: 6000000 INFO @ Tue, 16 Jun 2020 08:10:47: 12000000 INFO @ Tue, 16 Jun 2020 08:10:50: 7000000 INFO @ Tue, 16 Jun 2020 08:10:52: 13000000 INFO @ Tue, 16 Jun 2020 08:10:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:56: 8000000 INFO @ Tue, 16 Jun 2020 08:10:58: 14000000 INFO @ Tue, 16 Jun 2020 08:10:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:58: #1 total tags in treatment: 14163134 INFO @ Tue, 16 Jun 2020 08:10:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:58: #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 08:10:59: #1 tags after filtering in treatment: 14163134 INFO @ Tue, 16 Jun 2020 08:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:00: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:11:00: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:00: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:11:00: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 16 Jun 2020 08:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.10_model.r WARNING @ Tue, 16 Jun 2020 08:11:00: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:00: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 16 Jun 2020 08:11:00: #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 08:11:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:01: 9000000 INFO @ Tue, 16 Jun 2020 08:11:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:06: 10000000 INFO @ Tue, 16 Jun 2020 08:11:11: 11000000 INFO @ Tue, 16 Jun 2020 08:11:17: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:22: 13000000 INFO @ Tue, 16 Jun 2020 08:11:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:27: 14000000 INFO @ Tue, 16 Jun 2020 08:11:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:11:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:11:28: #1 total tags in treatment: 14163134 INFO @ Tue, 16 Jun 2020 08:11:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:28: #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 08:11:28: #1 tags after filtering in treatment: 14163134 INFO @ Tue, 16 Jun 2020 08:11:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:29: #2 number of paired peaks: 385 WARNING @ Tue, 16 Jun 2020 08:11:29: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:29: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:11:29: #2 alternative fragment length(s) may be 2,29 bps INFO @ Tue, 16 Jun 2020 08:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.20_model.r WARNING @ Tue, 16 Jun 2020 08:11:29: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:29: #2 You may need to consider one of the other alternative d(s): 2,29 WARNING @ Tue, 16 Jun 2020 08:11:29: #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 08:11:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX172527/SRX172527.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling