Job ID = 6507818 SRX = SRX494823 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:15:03 prefetch.2.10.7: 1) Downloading 'SRR1198355'... 2020-06-26T13:15:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:16:57 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:16:57 prefetch.2.10.7: 1) 'SRR1198355' was downloaded successfully Read 16505446 spots for SRR1198355/SRR1198355.sra Written 16505446 spots for SRR1198355/SRR1198355.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: 00:02:21 16505446 reads; of these: 16505446 (100.00%) were unpaired; of these: 4910053 (29.75%) aligned 0 times 9424381 (57.10%) aligned exactly 1 time 2171012 (13.15%) aligned >1 times 70.25% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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_rmdupse_core] 1085934 / 11595393 = 0.0937 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 22:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.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 22:23:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:23:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:23:19: 1000000 INFO @ Fri, 26 Jun 2020 22:23:25: 2000000 INFO @ Fri, 26 Jun 2020 22:23:30: 3000000 INFO @ Fri, 26 Jun 2020 22:23:35: 4000000 INFO @ Fri, 26 Jun 2020 22:23:40: 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 22:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.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 22:23:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:23:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:23:45: 6000000 INFO @ Fri, 26 Jun 2020 22:23:50: 1000000 INFO @ Fri, 26 Jun 2020 22:23:51: 7000000 INFO @ Fri, 26 Jun 2020 22:23:55: 2000000 INFO @ Fri, 26 Jun 2020 22:23:56: 8000000 INFO @ Fri, 26 Jun 2020 22:24:01: 3000000 INFO @ Fri, 26 Jun 2020 22:24:02: 9000000 INFO @ Fri, 26 Jun 2020 22:24:07: 4000000 INFO @ Fri, 26 Jun 2020 22:24:07: 10000000 INFO @ Fri, 26 Jun 2020 22:24:10: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:24:10: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:24:10: #1 total tags in treatment: 10509459 INFO @ Fri, 26 Jun 2020 22:24:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:24:10: #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 22:24:10: #1 tags after filtering in treatment: 10509459 INFO @ Fri, 26 Jun 2020 22:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:24:10: #1 finished! INFO @ Fri, 26 Jun 2020 22:24:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:24:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:24:11: #2 number of paired peaks: 304 WARNING @ Fri, 26 Jun 2020 22:24:11: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 26 Jun 2020 22:24:11: start model_add_line... INFO @ Fri, 26 Jun 2020 22:24:11: start X-correlation... INFO @ Fri, 26 Jun 2020 22:24:11: end of X-cor INFO @ Fri, 26 Jun 2020 22:24:11: #2 finished! INFO @ Fri, 26 Jun 2020 22:24:11: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:24:11: #2 alternative fragment length(s) may be 1,33,589 bps INFO @ Fri, 26 Jun 2020 22:24:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.05_model.r WARNING @ Fri, 26 Jun 2020 22:24:11: #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 22:24:11: #2 You may need to consider one of the other alternative d(s): 1,33,589 WARNING @ Fri, 26 Jun 2020 22:24:11: #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 22:24:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:24:11: #3 Pre-compute pvalue-qvalue table... 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 22:24:12: 5000000 INFO @ Fri, 26 Jun 2020 22:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.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 22:24:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:24:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:24:18: 6000000 INFO @ Fri, 26 Jun 2020 22:24:20: 1000000 INFO @ Fri, 26 Jun 2020 22:24:23: 7000000 INFO @ Fri, 26 Jun 2020 22:24:25: 2000000 INFO @ Fri, 26 Jun 2020 22:24:29: 8000000 INFO @ Fri, 26 Jun 2020 22:24:31: 3000000 INFO @ Fri, 26 Jun 2020 22:24:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:24:35: 9000000 INFO @ Fri, 26 Jun 2020 22:24:36: 4000000 INFO @ Fri, 26 Jun 2020 22:24:40: 10000000 INFO @ Fri, 26 Jun 2020 22:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.05_summits.bed INFO @ Fri, 26 Jun 2020 22:24:41: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:24:42: 5000000 INFO @ Fri, 26 Jun 2020 22:24:43: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:24:43: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:24:43: #1 total tags in treatment: 10509459 INFO @ Fri, 26 Jun 2020 22:24:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:24:43: #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 22:24:43: #1 tags after filtering in treatment: 10509459 INFO @ Fri, 26 Jun 2020 22:24:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:24:43: #1 finished! INFO @ Fri, 26 Jun 2020 22:24:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:24:44: #2 number of paired peaks: 304 WARNING @ Fri, 26 Jun 2020 22:24:44: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 26 Jun 2020 22:24:44: start model_add_line... INFO @ Fri, 26 Jun 2020 22:24:44: start X-correlation... INFO @ Fri, 26 Jun 2020 22:24:44: end of X-cor INFO @ Fri, 26 Jun 2020 22:24:44: #2 finished! INFO @ Fri, 26 Jun 2020 22:24:44: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:24:44: #2 alternative fragment length(s) may be 1,33,589 bps INFO @ Fri, 26 Jun 2020 22:24:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.10_model.r WARNING @ Fri, 26 Jun 2020 22:24:44: #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 22:24:44: #2 You may need to consider one of the other alternative d(s): 1,33,589 WARNING @ Fri, 26 Jun 2020 22:24:44: #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 22:24:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:24:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:24:47: 6000000 INFO @ Fri, 26 Jun 2020 22:24:53: 7000000 INFO @ Fri, 26 Jun 2020 22:24:58: 8000000 INFO @ Fri, 26 Jun 2020 22:25:03: 9000000 INFO @ Fri, 26 Jun 2020 22:25:03: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:25:08: 10000000 INFO @ Fri, 26 Jun 2020 22:25:11: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:25:11: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:25:11: #1 total tags in treatment: 10509459 INFO @ Fri, 26 Jun 2020 22:25:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:25:11: #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 22:25:11: #1 tags after filtering in treatment: 10509459 INFO @ Fri, 26 Jun 2020 22:25:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:25:11: #1 finished! INFO @ Fri, 26 Jun 2020 22:25:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:25:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:25:12: #2 number of paired peaks: 304 WARNING @ Fri, 26 Jun 2020 22:25:12: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 26 Jun 2020 22:25:12: start model_add_line... INFO @ Fri, 26 Jun 2020 22:25:12: start X-correlation... INFO @ Fri, 26 Jun 2020 22:25:12: end of X-cor INFO @ Fri, 26 Jun 2020 22:25:12: #2 finished! INFO @ Fri, 26 Jun 2020 22:25:12: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:25:12: #2 alternative fragment length(s) may be 1,33,589 bps INFO @ Fri, 26 Jun 2020 22:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.20_model.r WARNING @ Fri, 26 Jun 2020 22:25:12: #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 22:25:12: #2 You may need to consider one of the other alternative d(s): 1,33,589 WARNING @ Fri, 26 Jun 2020 22:25:12: #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 22:25:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.10_summits.bed INFO @ Fri, 26 Jun 2020 22:25:13: 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 @ Fri, 26 Jun 2020 22:25:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:25:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:25:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:25:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494823/SRX494823.20_summits.bed INFO @ Fri, 26 Jun 2020 22:25:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling