Job ID = 6507966 SRX = SRX495124 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:49:57 prefetch.2.10.7: 1) Downloading 'SRR1198656'... 2020-06-26T13:49:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:52:41 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:52:41 prefetch.2.10.7: 1) 'SRR1198656' was downloaded successfully Read 24225155 spots for SRR1198656/SRR1198656.sra Written 24225155 spots for SRR1198656/SRR1198656.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: 00:05:48 24225155 reads; of these: 24225155 (100.00%) were unpaired; of these: 1983567 (8.19%) aligned 0 times 18558329 (76.61%) aligned exactly 1 time 3683259 (15.20%) aligned >1 times 91.81% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 9070465 / 22241588 = 0.4078 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 @ Fri, 26 Jun 2020 23:05:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.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 @ Fri, 26 Jun 2020 23:05:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:05:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:05:23: 1000000 INFO @ Fri, 26 Jun 2020 23:05:28: 2000000 INFO @ Fri, 26 Jun 2020 23:05:34: 3000000 INFO @ Fri, 26 Jun 2020 23:05:39: 4000000 INFO @ Fri, 26 Jun 2020 23:05:45: 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 @ Fri, 26 Jun 2020 23:05:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.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 @ Fri, 26 Jun 2020 23:05:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:05:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:05:50: 6000000 INFO @ Fri, 26 Jun 2020 23:05:53: 1000000 INFO @ Fri, 26 Jun 2020 23:05:56: 7000000 INFO @ Fri, 26 Jun 2020 23:05:59: 2000000 INFO @ Fri, 26 Jun 2020 23:06:02: 8000000 INFO @ Fri, 26 Jun 2020 23:06:04: 3000000 INFO @ Fri, 26 Jun 2020 23:06:08: 9000000 INFO @ Fri, 26 Jun 2020 23:06:10: 4000000 INFO @ Fri, 26 Jun 2020 23:06:13: 10000000 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 @ Fri, 26 Jun 2020 23:06:16: 5000000 INFO @ Fri, 26 Jun 2020 23:06:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.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 @ Fri, 26 Jun 2020 23:06:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:06:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:06:19: 11000000 INFO @ Fri, 26 Jun 2020 23:06:21: 6000000 INFO @ Fri, 26 Jun 2020 23:06:23: 1000000 INFO @ Fri, 26 Jun 2020 23:06:25: 12000000 INFO @ Fri, 26 Jun 2020 23:06:27: 7000000 INFO @ Fri, 26 Jun 2020 23:06:29: 2000000 INFO @ Fri, 26 Jun 2020 23:06:31: 13000000 INFO @ Fri, 26 Jun 2020 23:06:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:06:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:06:32: #1 total tags in treatment: 13171123 INFO @ Fri, 26 Jun 2020 23:06:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:06:32: #1 tags after filtering in treatment: 13171123 INFO @ Fri, 26 Jun 2020 23:06:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:06:32: #1 finished! INFO @ Fri, 26 Jun 2020 23:06:32: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:06:33: 8000000 INFO @ Fri, 26 Jun 2020 23:06:33: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 23:06:33: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 23:06:33: start model_add_line... INFO @ Fri, 26 Jun 2020 23:06:33: start X-correlation... INFO @ Fri, 26 Jun 2020 23:06:33: end of X-cor INFO @ Fri, 26 Jun 2020 23:06:33: #2 finished! INFO @ Fri, 26 Jun 2020 23:06:33: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:06:33: #2 alternative fragment length(s) may be 1,42,580 bps INFO @ Fri, 26 Jun 2020 23:06:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.05_model.r WARNING @ Fri, 26 Jun 2020 23:06:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:06:33: #2 You may need to consider one of the other alternative d(s): 1,42,580 WARNING @ Fri, 26 Jun 2020 23:06:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:06:33: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:06:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:06:35: 3000000 INFO @ Fri, 26 Jun 2020 23:06:38: 9000000 INFO @ Fri, 26 Jun 2020 23:06:41: 4000000 INFO @ Fri, 26 Jun 2020 23:06:44: 10000000 INFO @ Fri, 26 Jun 2020 23:06:46: 5000000 INFO @ Fri, 26 Jun 2020 23:06:50: 11000000 INFO @ Fri, 26 Jun 2020 23:06:52: 6000000 INFO @ Fri, 26 Jun 2020 23:06:57: 12000000 INFO @ Fri, 26 Jun 2020 23:06:58: 7000000 INFO @ Fri, 26 Jun 2020 23:07:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:07:03: 13000000 INFO @ Fri, 26 Jun 2020 23:07:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:07:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:07:04: #1 total tags in treatment: 13171123 INFO @ Fri, 26 Jun 2020 23:07:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:07:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:07:04: #1 tags after filtering in treatment: 13171123 INFO @ Fri, 26 Jun 2020 23:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:07:04: #1 finished! INFO @ Fri, 26 Jun 2020 23:07:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:07:05: 8000000 INFO @ Fri, 26 Jun 2020 23:07:05: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 23:07:05: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 23:07:05: start model_add_line... INFO @ Fri, 26 Jun 2020 23:07:05: start X-correlation... INFO @ Fri, 26 Jun 2020 23:07:05: end of X-cor INFO @ Fri, 26 Jun 2020 23:07:05: #2 finished! INFO @ Fri, 26 Jun 2020 23:07:05: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:07:05: #2 alternative fragment length(s) may be 1,42,580 bps INFO @ Fri, 26 Jun 2020 23:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.10_model.r WARNING @ Fri, 26 Jun 2020 23:07:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:07:05: #2 You may need to consider one of the other alternative d(s): 1,42,580 WARNING @ Fri, 26 Jun 2020 23:07:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:07:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:07:10: 9000000 INFO @ Fri, 26 Jun 2020 23:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.05_summits.bed INFO @ Fri, 26 Jun 2020 23:07:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:07:17: 10000000 INFO @ Fri, 26 Jun 2020 23:07:22: 11000000 INFO @ Fri, 26 Jun 2020 23:07:28: 12000000 INFO @ Fri, 26 Jun 2020 23:07:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:07:34: 13000000 INFO @ Fri, 26 Jun 2020 23:07:35: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:07:35: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:07:35: #1 total tags in treatment: 13171123 INFO @ Fri, 26 Jun 2020 23:07:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:07:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:07:36: #1 tags after filtering in treatment: 13171123 INFO @ Fri, 26 Jun 2020 23:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:07:36: #1 finished! INFO @ Fri, 26 Jun 2020 23:07:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:07:37: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 23:07:37: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 23:07:37: start model_add_line... INFO @ Fri, 26 Jun 2020 23:07:37: start X-correlation... INFO @ Fri, 26 Jun 2020 23:07:37: end of X-cor INFO @ Fri, 26 Jun 2020 23:07:37: #2 finished! INFO @ Fri, 26 Jun 2020 23:07:37: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:07:37: #2 alternative fragment length(s) may be 1,42,580 bps INFO @ Fri, 26 Jun 2020 23:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.20_model.r WARNING @ Fri, 26 Jun 2020 23:07:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:07:37: #2 You may need to consider one of the other alternative d(s): 1,42,580 WARNING @ Fri, 26 Jun 2020 23:07:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:07:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:07:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.10_summits.bed INFO @ Fri, 26 Jun 2020 23:07:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:08:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:08:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:08:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:08:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495124/SRX495124.20_summits.bed INFO @ Fri, 26 Jun 2020 23:08:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling