Job ID = 6366429 SRX = SRX146469 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:26 prefetch.2.10.7: 1) Downloading 'SRR494630'... 2020-06-15T22:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:57 prefetch.2.10.7: 'SRR494630' is valid 2020-06-15T22:50:57 prefetch.2.10.7: 1) 'SRR494630' was downloaded successfully Read 5185898 spots for SRR494630/SRR494630.sra Written 5185898 spots for SRR494630/SRR494630.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: 00:00:41 5185898 reads; of these: 5185898 (100.00%) were unpaired; of these: 2016242 (38.88%) aligned 0 times 2597843 (50.09%) aligned exactly 1 time 571813 (11.03%) aligned >1 times 61.12% overall alignment rate Time searching: 00:00:41 Overall time: 00:00:41 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] 120356 / 3169656 = 0.0380 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 07:52:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.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 07:52:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:03: 1000000 INFO @ Tue, 16 Jun 2020 07:53:08: 2000000 INFO @ Tue, 16 Jun 2020 07:53:13: 3000000 INFO @ Tue, 16 Jun 2020 07:53:14: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:14: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:14: #1 total tags in treatment: 3049300 INFO @ Tue, 16 Jun 2020 07:53:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:14: #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 07:53:14: #1 tags after filtering in treatment: 3049300 INFO @ Tue, 16 Jun 2020 07:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:14: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:14: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 07:53:14: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:14: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:53:14: #2 alternative fragment length(s) may be 33,445,564,594 bps INFO @ Tue, 16 Jun 2020 07:53:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.05_model.r WARNING @ Tue, 16 Jun 2020 07:53:14: #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 07:53:14: #2 You may need to consider one of the other alternative d(s): 33,445,564,594 WARNING @ Tue, 16 Jun 2020 07:53:14: #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 07:53:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 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 07:53:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.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 07:53:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:34: 1000000 INFO @ Tue, 16 Jun 2020 07:53:39: 2000000 INFO @ Tue, 16 Jun 2020 07:53:45: 3000000 INFO @ Tue, 16 Jun 2020 07:53:45: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:45: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:45: #1 total tags in treatment: 3049300 INFO @ Tue, 16 Jun 2020 07:53:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:45: #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 07:53:46: #1 tags after filtering in treatment: 3049300 INFO @ Tue, 16 Jun 2020 07:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:46: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 07:53:46: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 07:53:46: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:46: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:46: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:46: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:46: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:53:46: #2 alternative fragment length(s) may be 33,445,564,594 bps INFO @ Tue, 16 Jun 2020 07:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.10_model.r WARNING @ Tue, 16 Jun 2020 07:53:46: #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 07:53:46: #2 You may need to consider one of the other alternative d(s): 33,445,564,594 WARNING @ Tue, 16 Jun 2020 07:53:46: #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 07:53:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:53: #3 Call peaks for each chromosome... 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 07:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.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 07:53:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:54:03: 1000000 INFO @ Tue, 16 Jun 2020 07:54:08: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:13: 3000000 INFO @ Tue, 16 Jun 2020 07:54:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:54:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:54:13: #1 total tags in treatment: 3049300 INFO @ Tue, 16 Jun 2020 07:54:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:13: #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 07:54:13: #1 tags after filtering in treatment: 3049300 INFO @ Tue, 16 Jun 2020 07:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:14: #2 number of paired peaks: 428 WARNING @ Tue, 16 Jun 2020 07:54:14: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 16 Jun 2020 07:54:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:14: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:54:14: #2 alternative fragment length(s) may be 33,445,564,594 bps INFO @ Tue, 16 Jun 2020 07:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.20_model.r WARNING @ Tue, 16 Jun 2020 07:54:14: #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 07:54:14: #2 You may need to consider one of the other alternative d(s): 33,445,564,594 WARNING @ Tue, 16 Jun 2020 07:54:14: #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 07:54:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX146469/SRX146469.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (55 records, 4 fields): 2 millis CompletedMACS2peakCalling