Job ID = 6366186 SRX = SRX065711 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:31 prefetch.2.10.7: 1) Downloading 'SRR217417'... 2020-06-15T23:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:23:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:23:59 prefetch.2.10.7: 'SRR217417' is valid 2020-06-15T23:23:59 prefetch.2.10.7: 1) 'SRR217417' was downloaded successfully Read 7009834 spots for SRR217417/SRR217417.sra Written 7009834 spots for SRR217417/SRR217417.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: 00:01:08 7009834 reads; of these: 7009834 (100.00%) were unpaired; of these: 3440453 (49.08%) aligned 0 times 2981359 (42.53%) aligned exactly 1 time 588022 (8.39%) aligned >1 times 50.92% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 144308 / 3569381 = 0.0404 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 08:26:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.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 08:26:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:03: 1000000 INFO @ Tue, 16 Jun 2020 08:27:11: 2000000 INFO @ Tue, 16 Jun 2020 08:27:19: 3000000 INFO @ Tue, 16 Jun 2020 08:27:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:22: #1 total tags in treatment: 3425073 INFO @ Tue, 16 Jun 2020 08:27:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:22: #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 08:27:22: #1 tags after filtering in treatment: 3425073 INFO @ Tue, 16 Jun 2020 08:27:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:22: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 08:27:22: 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 08:27:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:22: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:27:22: #2 alternative fragment length(s) may be 4,34,483 bps INFO @ Tue, 16 Jun 2020 08:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:22: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:22: #2 You may need to consider one of the other alternative d(s): 4,34,483 WARNING @ Tue, 16 Jun 2020 08:27:22: #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 08:27:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:22: #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 08:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.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 08:27:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:27:33: 1000000 INFO @ Tue, 16 Jun 2020 08:27:41: 2000000 INFO @ Tue, 16 Jun 2020 08:27:49: 3000000 INFO @ Tue, 16 Jun 2020 08:27:52: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:27:52: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:27:52: #1 total tags in treatment: 3425073 INFO @ Tue, 16 Jun 2020 08:27:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:52: #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 08:27:52: #1 tags after filtering in treatment: 3425073 INFO @ Tue, 16 Jun 2020 08:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:52: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 08:27:52: 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 08:27:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:52: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:27:52: #2 alternative fragment length(s) may be 4,34,483 bps INFO @ Tue, 16 Jun 2020 08:27:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.10_model.r WARNING @ Tue, 16 Jun 2020 08:27:52: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:52: #2 You may need to consider one of the other alternative d(s): 4,34,483 WARNING @ Tue, 16 Jun 2020 08:27:52: #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 08:27:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:52: #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 08:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.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 08:27:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.10_summits.bed INFO @ Tue, 16 Jun 2020 08:28:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:03: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:11: 2000000 INFO @ Tue, 16 Jun 2020 08:28:19: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:22: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:28:22: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:28:22: #1 total tags in treatment: 3425073 INFO @ Tue, 16 Jun 2020 08:28:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:22: #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 08:28:22: #1 tags after filtering in treatment: 3425073 INFO @ Tue, 16 Jun 2020 08:28:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:22: #2 number of paired peaks: 387 WARNING @ Tue, 16 Jun 2020 08:28:22: 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 08:28:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:22: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:28:22: #2 alternative fragment length(s) may be 4,34,483 bps INFO @ Tue, 16 Jun 2020 08:28:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:22: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:22: #2 You may need to consider one of the other alternative d(s): 4,34,483 WARNING @ Tue, 16 Jun 2020 08:28:22: #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 08:28:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065711/SRX065711.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling