Job ID = 6368024 SRX = SRX466487 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:39 prefetch.2.10.7: 1) Downloading 'SRR1163553'... 2020-06-16T00:06:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:29 prefetch.2.10.7: 'SRR1163553' is valid 2020-06-16T00:07:29 prefetch.2.10.7: 1) 'SRR1163553' was downloaded successfully Read 2533543 spots for SRR1163553/SRR1163553.sra Written 2533543 spots for SRR1163553/SRR1163553.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: 00:00:36 2533543 reads; of these: 2533543 (100.00%) were unpaired; of these: 215100 (8.49%) aligned 0 times 1800095 (71.05%) aligned exactly 1 time 518348 (20.46%) aligned >1 times 91.51% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 390816 / 2318443 = 0.1686 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 09:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.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 09:09:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:26: 1000000 INFO @ Tue, 16 Jun 2020 09:09:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:09:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:09:32: #1 total tags in treatment: 1927627 INFO @ Tue, 16 Jun 2020 09:09:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:32: #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 09:09:32: #1 tags after filtering in treatment: 1927627 INFO @ Tue, 16 Jun 2020 09:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:32: #2 number of paired peaks: 589 WARNING @ Tue, 16 Jun 2020 09:09:32: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:32: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:09:32: #2 alternative fragment length(s) may be 50,428,466,485,496 bps INFO @ Tue, 16 Jun 2020 09:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.05_model.r WARNING @ Tue, 16 Jun 2020 09:09:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:32: #2 You may need to consider one of the other alternative d(s): 50,428,466,485,496 WARNING @ Tue, 16 Jun 2020 09:09:32: #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 09:09:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.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 09:09:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:56: 1000000 INFO @ Tue, 16 Jun 2020 09:10:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:03: #1 total tags in treatment: 1927627 INFO @ Tue, 16 Jun 2020 09:10:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:03: #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 09:10:03: #1 tags after filtering in treatment: 1927627 INFO @ Tue, 16 Jun 2020 09:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:03: #2 number of paired peaks: 589 WARNING @ Tue, 16 Jun 2020 09:10:03: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:03: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:10:03: #2 alternative fragment length(s) may be 50,428,466,485,496 bps INFO @ Tue, 16 Jun 2020 09:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:03: #2 You may need to consider one of the other alternative d(s): 50,428,466,485,496 WARNING @ Tue, 16 Jun 2020 09:10:03: #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 09:10:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 09:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.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 09:10:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:26: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:10:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:32: #1 total tags in treatment: 1927627 INFO @ Tue, 16 Jun 2020 09:10:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:32: #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 09:10:32: #1 tags after filtering in treatment: 1927627 INFO @ Tue, 16 Jun 2020 09:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:32: #2 number of paired peaks: 589 WARNING @ Tue, 16 Jun 2020 09:10:32: Fewer paired peaks (589) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 589 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:32: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:10:32: #2 alternative fragment length(s) may be 50,428,466,485,496 bps INFO @ Tue, 16 Jun 2020 09:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.20_model.r WARNING @ Tue, 16 Jun 2020 09:10:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:32: #2 You may need to consider one of the other alternative d(s): 50,428,466,485,496 WARNING @ Tue, 16 Jun 2020 09:10:32: #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 09:10:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466487/SRX466487.20_summits.bed INFO @ Tue, 16 Jun 2020 09:10:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis CompletedMACS2peakCalling