Job ID = 6497414 SRX = SRX494826 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:26:11 prefetch.2.10.7: 1) Downloading 'SRR1198358'... 2020-06-25T22:26:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:27:37 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:27:38 prefetch.2.10.7: 'SRR1198358' is valid 2020-06-25T22:27:38 prefetch.2.10.7: 1) 'SRR1198358' was downloaded successfully Read 16052001 spots for SRR1198358/SRR1198358.sra Written 16052001 spots for SRR1198358/SRR1198358.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: 00:02:09 16052001 reads; of these: 16052001 (100.00%) were unpaired; of these: 5228842 (32.57%) aligned 0 times 8838603 (55.06%) aligned exactly 1 time 1984556 (12.36%) aligned >1 times 67.43% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 1604340 / 10823159 = 0.1482 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 07:33:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.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 07:33:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:17: 1000000 INFO @ Fri, 26 Jun 2020 07:33:24: 2000000 INFO @ Fri, 26 Jun 2020 07:33:31: 3000000 INFO @ Fri, 26 Jun 2020 07:33:38: 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 @ Fri, 26 Jun 2020 07:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.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 07:33:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:45: 5000000 INFO @ Fri, 26 Jun 2020 07:33:48: 1000000 INFO @ Fri, 26 Jun 2020 07:33:52: 6000000 INFO @ Fri, 26 Jun 2020 07:33:55: 2000000 INFO @ Fri, 26 Jun 2020 07:34:00: 7000000 INFO @ Fri, 26 Jun 2020 07:34:03: 3000000 INFO @ Fri, 26 Jun 2020 07:34:07: 8000000 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 07:34:10: 4000000 INFO @ Fri, 26 Jun 2020 07:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.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 07:34:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:34:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:15: 9000000 INFO @ Fri, 26 Jun 2020 07:34:17: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:34:17: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:34:17: #1 total tags in treatment: 9218819 INFO @ Fri, 26 Jun 2020 07:34:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:17: #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 07:34:17: #1 tags after filtering in treatment: 9218819 INFO @ Fri, 26 Jun 2020 07:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:17: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:17: 5000000 INFO @ Fri, 26 Jun 2020 07:34:18: #2 number of paired peaks: 402 WARNING @ Fri, 26 Jun 2020 07:34:18: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:18: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:18: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:18: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:18: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:18: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 07:34:18: #2 alternative fragment length(s) may be 2,38,583 bps INFO @ Fri, 26 Jun 2020 07:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.05_model.r WARNING @ Fri, 26 Jun 2020 07:34:18: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:34:18: #2 You may need to consider one of the other alternative d(s): 2,38,583 WARNING @ Fri, 26 Jun 2020 07:34:18: #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 07:34:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:18: 1000000 INFO @ Fri, 26 Jun 2020 07:34:25: 6000000 INFO @ Fri, 26 Jun 2020 07:34:25: 2000000 INFO @ Fri, 26 Jun 2020 07:34:32: 7000000 INFO @ Fri, 26 Jun 2020 07:34:32: 3000000 INFO @ Fri, 26 Jun 2020 07:34:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:40: 4000000 INFO @ Fri, 26 Jun 2020 07:34:40: 8000000 INFO @ Fri, 26 Jun 2020 07:34:47: 5000000 INFO @ Fri, 26 Jun 2020 07:34:48: 9000000 INFO @ Fri, 26 Jun 2020 07:34:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.05_summits.bed INFO @ Fri, 26 Jun 2020 07:34:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (931 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:49: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:34:49: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:34:49: #1 total tags in treatment: 9218819 INFO @ Fri, 26 Jun 2020 07:34:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:49: #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 07:34:49: #1 tags after filtering in treatment: 9218819 INFO @ Fri, 26 Jun 2020 07:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:49: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:50: #2 number of paired peaks: 402 WARNING @ Fri, 26 Jun 2020 07:34:50: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:50: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:50: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:50: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:50: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:50: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 07:34:50: #2 alternative fragment length(s) may be 2,38,583 bps INFO @ Fri, 26 Jun 2020 07:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.10_model.r WARNING @ Fri, 26 Jun 2020 07:34:50: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:34:50: #2 You may need to consider one of the other alternative d(s): 2,38,583 WARNING @ Fri, 26 Jun 2020 07:34:50: #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 07:34:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:34:54: 6000000 INFO @ Fri, 26 Jun 2020 07:35:00: 7000000 INFO @ Fri, 26 Jun 2020 07:35:07: 8000000 INFO @ Fri, 26 Jun 2020 07:35:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:35:14: 9000000 INFO @ Fri, 26 Jun 2020 07:35:15: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:35:15: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:35:15: #1 total tags in treatment: 9218819 INFO @ Fri, 26 Jun 2020 07:35:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:15: #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 07:35:15: #1 tags after filtering in treatment: 9218819 INFO @ Fri, 26 Jun 2020 07:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:16: #2 number of paired peaks: 402 WARNING @ Fri, 26 Jun 2020 07:35:16: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:16: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:16: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:16: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:16: #2 predicted fragment length is 38 bps INFO @ Fri, 26 Jun 2020 07:35:16: #2 alternative fragment length(s) may be 2,38,583 bps INFO @ Fri, 26 Jun 2020 07:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.20_model.r WARNING @ Fri, 26 Jun 2020 07:35:16: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:35:16: #2 You may need to consider one of the other alternative d(s): 2,38,583 WARNING @ Fri, 26 Jun 2020 07:35:16: #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 07:35:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.10_summits.bed INFO @ Fri, 26 Jun 2020 07:35:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (416 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494826/SRX494826.20_summits.bed INFO @ Fri, 26 Jun 2020 07:35:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling