Job ID = 6367374 SRX = SRX331133 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:24:46 prefetch.2.10.7: 1) Downloading 'SRR947364'... 2020-06-15T23:24:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:25:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:25:14 prefetch.2.10.7: 'SRR947364' is valid 2020-06-15T23:25:14 prefetch.2.10.7: 1) 'SRR947364' was downloaded successfully Read 9306870 spots for SRR947364/SRR947364.sra Written 9306870 spots for SRR947364/SRR947364.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: 00:01:23 9306870 reads; of these: 9306870 (100.00%) were unpaired; of these: 104993 (1.13%) aligned 0 times 7966989 (85.60%) aligned exactly 1 time 1234888 (13.27%) aligned >1 times 98.87% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 1585330 / 9201877 = 0.1723 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 08:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.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 08:29:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:26: 1000000 INFO @ Tue, 16 Jun 2020 08:29:31: 2000000 INFO @ Tue, 16 Jun 2020 08:29:37: 3000000 INFO @ Tue, 16 Jun 2020 08:29:42: 4000000 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 08:29:48: 5000000 INFO @ Tue, 16 Jun 2020 08:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.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 08:29:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:29:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:29:54: 6000000 INFO @ Tue, 16 Jun 2020 08:29:56: 1000000 INFO @ Tue, 16 Jun 2020 08:30:00: 7000000 INFO @ Tue, 16 Jun 2020 08:30:02: 2000000 INFO @ Tue, 16 Jun 2020 08:30:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:03: #1 total tags in treatment: 7616547 INFO @ Tue, 16 Jun 2020 08:30:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:03: #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 08:30:03: #1 tags after filtering in treatment: 7616547 INFO @ Tue, 16 Jun 2020 08:30:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:04: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 08:30:04: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:04: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:30:04: #2 alternative fragment length(s) may be 2,30,62,588 bps INFO @ Tue, 16 Jun 2020 08:30:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.05_model.r WARNING @ Tue, 16 Jun 2020 08:30:04: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:04: #2 You may need to consider one of the other alternative d(s): 2,30,62,588 WARNING @ Tue, 16 Jun 2020 08:30:04: #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 08:30:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:08: 3000000 INFO @ Tue, 16 Jun 2020 08:30:14: 4000000 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 08:30:20: 5000000 INFO @ Tue, 16 Jun 2020 08:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.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 08:30:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:26: 1000000 INFO @ Tue, 16 Jun 2020 08:30:26: 6000000 INFO @ Tue, 16 Jun 2020 08:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.05_summits.bed INFO @ Tue, 16 Jun 2020 08:30:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:32: 2000000 INFO @ Tue, 16 Jun 2020 08:30:32: 7000000 INFO @ Tue, 16 Jun 2020 08:30:36: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:30:36: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:30:36: #1 total tags in treatment: 7616547 INFO @ Tue, 16 Jun 2020 08:30:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:30:36: #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 08:30:36: #1 tags after filtering in treatment: 7616547 INFO @ Tue, 16 Jun 2020 08:30:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:30:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:30:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:30:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:30:37: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 08:30:37: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 08:30:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:30:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:30:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:30:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:30:37: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:30:37: #2 alternative fragment length(s) may be 2,30,62,588 bps INFO @ Tue, 16 Jun 2020 08:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.10_model.r WARNING @ Tue, 16 Jun 2020 08:30:37: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:30:37: #2 You may need to consider one of the other alternative d(s): 2,30,62,588 WARNING @ Tue, 16 Jun 2020 08:30:37: #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 08:30:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:30:38: 3000000 INFO @ Tue, 16 Jun 2020 08:30:43: 4000000 INFO @ Tue, 16 Jun 2020 08:30:49: 5000000 INFO @ Tue, 16 Jun 2020 08:30:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:54: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:31:00: 7000000 INFO @ Tue, 16 Jun 2020 08:31:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.10_summits.bed INFO @ Tue, 16 Jun 2020 08:31:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:31:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:31:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:31:03: #1 total tags in treatment: 7616547 INFO @ Tue, 16 Jun 2020 08:31:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:31:03: #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 08:31:04: #1 tags after filtering in treatment: 7616547 INFO @ Tue, 16 Jun 2020 08:31:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:31:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:31:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:31:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:31:04: #2 number of paired peaks: 363 WARNING @ Tue, 16 Jun 2020 08:31:04: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Tue, 16 Jun 2020 08:31:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:31:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:31:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:31:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:31:04: #2 predicted fragment length is 30 bps INFO @ Tue, 16 Jun 2020 08:31:04: #2 alternative fragment length(s) may be 2,30,62,588 bps INFO @ Tue, 16 Jun 2020 08:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.20_model.r WARNING @ Tue, 16 Jun 2020 08:31:04: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:31:04: #2 You may need to consider one of the other alternative d(s): 2,30,62,588 WARNING @ Tue, 16 Jun 2020 08:31:04: #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 08:31:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:31:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:31:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:31:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:31:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:31:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331133/SRX331133.20_summits.bed INFO @ Tue, 16 Jun 2020 08:31:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (51 records, 4 fields): 0 millis CompletedMACS2peakCalling