Job ID = 6365861 SRX = SRX003827 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:10:27 prefetch.2.10.7: 1) Downloading 'SRR015067'... 2020-06-15T22:10:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:12:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:12:27 prefetch.2.10.7: 'SRR015067' is valid 2020-06-15T22:12:27 prefetch.2.10.7: 1) 'SRR015067' was downloaded successfully Read 2362213 spots for SRR015067/SRR015067.sra Written 2362213 spots for SRR015067/SRR015067.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: 00:00:01 Multiseed full-index search: 00:00:13 2362213 reads; of these: 2362213 (100.00%) were unpaired; of these: 1590872 (67.35%) aligned 0 times 561676 (23.78%) aligned exactly 1 time 209665 (8.88%) aligned >1 times 32.65% overall alignment rate Time searching: 00:00:14 Overall time: 00:00:14 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] 168349 / 771341 = 0.2183 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 07:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.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 07:13:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:13:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:13:28: #1 tag size is determined as 33 bps INFO @ Tue, 16 Jun 2020 07:13:28: #1 tag size = 33 INFO @ Tue, 16 Jun 2020 07:13:28: #1 total tags in treatment: 602992 INFO @ Tue, 16 Jun 2020 07:13:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:13:28: #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 07:13:28: #1 tags after filtering in treatment: 602992 INFO @ Tue, 16 Jun 2020 07:13:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:13:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:13:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:13:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:13:28: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 07:13:28: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 07:13:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:13:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:13:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:13:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:13:28: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:13:28: #2 alternative fragment length(s) may be 38,63,144,542,578 bps INFO @ Tue, 16 Jun 2020 07:13:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.05_model.r WARNING @ Tue, 16 Jun 2020 07:13:28: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:13:28: #2 You may need to consider one of the other alternative d(s): 38,63,144,542,578 WARNING @ Tue, 16 Jun 2020 07:13:28: #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 07:13:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:13:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:13:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.05_summits.bed INFO @ Tue, 16 Jun 2020 07:13:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (358 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 07:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.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 07:13:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:13:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:13:58: #1 tag size is determined as 33 bps INFO @ Tue, 16 Jun 2020 07:13:58: #1 tag size = 33 INFO @ Tue, 16 Jun 2020 07:13:58: #1 total tags in treatment: 602992 INFO @ Tue, 16 Jun 2020 07:13:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:13:58: #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 07:13:58: #1 tags after filtering in treatment: 602992 INFO @ Tue, 16 Jun 2020 07:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:13:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:13:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:13:58: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 07:13:58: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 07:13:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:13:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:13:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:13:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:13:58: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:13:58: #2 alternative fragment length(s) may be 38,63,144,542,578 bps INFO @ Tue, 16 Jun 2020 07:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.10_model.r WARNING @ Tue, 16 Jun 2020 07:13:58: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:13:58: #2 You may need to consider one of the other alternative d(s): 38,63,144,542,578 WARNING @ Tue, 16 Jun 2020 07:13:58: #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 07:13:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:13:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.10_summits.bed INFO @ Tue, 16 Jun 2020 07:14:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (158 records, 4 fields): 1 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 07:14:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.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 07:14:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:14:25: #1 read treatment tags... 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 07:14:28: #1 tag size is determined as 33 bps INFO @ Tue, 16 Jun 2020 07:14:28: #1 tag size = 33 INFO @ Tue, 16 Jun 2020 07:14:28: #1 total tags in treatment: 602992 INFO @ Tue, 16 Jun 2020 07:14:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:14:28: #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 07:14:28: #1 tags after filtering in treatment: 602992 INFO @ Tue, 16 Jun 2020 07:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:14:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:14:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:14:28: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 07:14:28: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 07:14:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:14:28: start X-correlation... INFO @ Tue, 16 Jun 2020 07:14:28: end of X-cor INFO @ Tue, 16 Jun 2020 07:14:28: #2 finished! INFO @ Tue, 16 Jun 2020 07:14:28: #2 predicted fragment length is 38 bps INFO @ Tue, 16 Jun 2020 07:14:28: #2 alternative fragment length(s) may be 38,63,144,542,578 bps INFO @ Tue, 16 Jun 2020 07:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.20_model.r WARNING @ Tue, 16 Jun 2020 07:14:28: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:14:28: #2 You may need to consider one of the other alternative d(s): 38,63,144,542,578 WARNING @ Tue, 16 Jun 2020 07:14:28: #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 07:14:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:14:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX003827/SRX003827.20_summits.bed INFO @ Tue, 16 Jun 2020 07:14:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 0 millis CompletedMACS2peakCalling