Job ID = 6366191 SRX = SRX065716 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:22:30 prefetch.2.10.7: 1) Downloading 'SRR217422'... 2020-06-15T22:22:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:22:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:22:54 prefetch.2.10.7: 'SRR217422' is valid 2020-06-15T22:22:54 prefetch.2.10.7: 1) 'SRR217422' was downloaded successfully Read 4537084 spots for SRR217422/SRR217422.sra Written 4537084 spots for SRR217422/SRR217422.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: 00:00:45 4537084 reads; of these: 4537084 (100.00%) were unpaired; of these: 705216 (15.54%) aligned 0 times 3222397 (71.02%) aligned exactly 1 time 609471 (13.43%) aligned >1 times 84.46% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 194040 / 3831868 = 0.0506 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 07:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.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 07:25:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:14: 1000000 INFO @ Tue, 16 Jun 2020 07:25:21: 2000000 INFO @ Tue, 16 Jun 2020 07:25:27: 3000000 INFO @ Tue, 16 Jun 2020 07:25:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:25:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:25:31: #1 total tags in treatment: 3637828 INFO @ Tue, 16 Jun 2020 07:25:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:31: #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 07:25:31: #1 tags after filtering in treatment: 3637828 INFO @ Tue, 16 Jun 2020 07:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:32: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 07:25:32: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Tue, 16 Jun 2020 07:25:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:32: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:25:32: #2 alternative fragment length(s) may be 4,33,553,567,587 bps INFO @ Tue, 16 Jun 2020 07:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.05_model.r WARNING @ Tue, 16 Jun 2020 07:25:32: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:25:32: #2 You may need to consider one of the other alternative d(s): 4,33,553,567,587 WARNING @ Tue, 16 Jun 2020 07:25:32: #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 07:25:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:32: #3 Pre-compute pvalue-qvalue table... 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 07:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.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 07:25:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:25:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:25:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:25:43: 1000000 INFO @ Tue, 16 Jun 2020 07:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.05_summits.bed INFO @ Tue, 16 Jun 2020 07:25:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (364 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:25:49: 2000000 INFO @ Tue, 16 Jun 2020 07:25:55: 3000000 INFO @ Tue, 16 Jun 2020 07:25:59: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:25:59: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:25:59: #1 total tags in treatment: 3637828 INFO @ Tue, 16 Jun 2020 07:25:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:25:59: #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 07:25:59: #1 tags after filtering in treatment: 3637828 INFO @ Tue, 16 Jun 2020 07:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:25:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:25:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:25:59: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 07:25:59: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Tue, 16 Jun 2020 07:25:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:25:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:25:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:25:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:25:59: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:25:59: #2 alternative fragment length(s) may be 4,33,553,567,587 bps INFO @ Tue, 16 Jun 2020 07:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.10_model.r WARNING @ Tue, 16 Jun 2020 07:25:59: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:25:59: #2 You may need to consider one of the other alternative d(s): 4,33,553,567,587 WARNING @ Tue, 16 Jun 2020 07:25:59: #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 07:25:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:25:59: #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 @ Tue, 16 Jun 2020 07:26:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.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 07:26:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:26:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:26:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.10_summits.bed INFO @ Tue, 16 Jun 2020 07:26:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:26:14: 1000000 INFO @ Tue, 16 Jun 2020 07:26:19: 2000000 INFO @ Tue, 16 Jun 2020 07:26:25: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:26:28: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:26:28: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:26:28: #1 total tags in treatment: 3637828 INFO @ Tue, 16 Jun 2020 07:26:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:26:28: #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 07:26:28: #1 tags after filtering in treatment: 3637828 INFO @ Tue, 16 Jun 2020 07:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:26:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:26:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:26:28: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 07:26:28: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Tue, 16 Jun 2020 07:26:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:26:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:26:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:26:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:26:29: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:26:29: #2 alternative fragment length(s) may be 4,33,553,567,587 bps INFO @ Tue, 16 Jun 2020 07:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.20_model.r WARNING @ Tue, 16 Jun 2020 07:26:29: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:26:29: #2 You may need to consider one of the other alternative d(s): 4,33,553,567,587 WARNING @ Tue, 16 Jun 2020 07:26:29: #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 07:26:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:26:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:26:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065716/SRX065716.20_summits.bed INFO @ Tue, 16 Jun 2020 07:26:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (39 records, 4 fields): 2 millis CompletedMACS2peakCalling