Job ID = 6366716 SRX = SRX2228870 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:51:26 prefetch.2.10.7: 1) Downloading 'SRR4380326'... 2020-06-15T22:51:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:26 prefetch.2.10.7: 'SRR4380326' is valid 2020-06-15T22:52:26 prefetch.2.10.7: 1) 'SRR4380326' was downloaded successfully Read 9142363 spots for SRR4380326/SRR4380326.sra Written 9142363 spots for SRR4380326/SRR4380326.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: 00:02:03 9142363 reads; of these: 9142363 (100.00%) were unpaired; of these: 169376 (1.85%) aligned 0 times 7409669 (81.05%) aligned exactly 1 time 1563318 (17.10%) aligned >1 times 98.15% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 550425 / 8972987 = 0.0613 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 07:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.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 07:57:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:57:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:57:40: 1000000 INFO @ Tue, 16 Jun 2020 07:57:45: 2000000 INFO @ Tue, 16 Jun 2020 07:57:51: 3000000 INFO @ Tue, 16 Jun 2020 07:57:57: 4000000 INFO @ Tue, 16 Jun 2020 07:58:02: 5000000 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 07:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.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 07:58:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:08: 6000000 INFO @ Tue, 16 Jun 2020 07:58:10: 1000000 INFO @ Tue, 16 Jun 2020 07:58:14: 7000000 INFO @ Tue, 16 Jun 2020 07:58:16: 2000000 INFO @ Tue, 16 Jun 2020 07:58:20: 8000000 INFO @ Tue, 16 Jun 2020 07:58:22: 3000000 INFO @ Tue, 16 Jun 2020 07:58:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:58:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:58:22: #1 total tags in treatment: 8422562 INFO @ Tue, 16 Jun 2020 07:58:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:22: #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 07:58:22: #1 tags after filtering in treatment: 8422562 INFO @ Tue, 16 Jun 2020 07:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:22: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:23: #2 number of paired peaks: 299 WARNING @ Tue, 16 Jun 2020 07:58:23: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:23: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:23: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:23: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:23: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:23: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:58:23: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 07:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.05_model.r WARNING @ Tue, 16 Jun 2020 07:58:23: #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 07:58:23: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 07:58:23: #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 07:58:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:27: 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 07:58:33: 5000000 INFO @ Tue, 16 Jun 2020 07:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.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 07:58:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:58:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:58:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:58:40: 6000000 INFO @ Tue, 16 Jun 2020 07:58:42: 1000000 INFO @ Tue, 16 Jun 2020 07:58:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.05_summits.bed INFO @ Tue, 16 Jun 2020 07:58:47: Done! INFO @ Tue, 16 Jun 2020 07:58:47: 7000000 pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (562 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:58:49: 2000000 INFO @ Tue, 16 Jun 2020 07:58:54: 8000000 INFO @ Tue, 16 Jun 2020 07:58:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:58:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:58:57: #1 total tags in treatment: 8422562 INFO @ Tue, 16 Jun 2020 07:58:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:57: #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 07:58:57: #1 tags after filtering in treatment: 8422562 INFO @ Tue, 16 Jun 2020 07:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:57: #2 number of paired peaks: 299 WARNING @ Tue, 16 Jun 2020 07:58:57: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:57: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:58:57: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 07:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.10_model.r WARNING @ Tue, 16 Jun 2020 07:58:57: #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 07:58:57: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 07:58:57: #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 07:58:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:57: 3000000 INFO @ Tue, 16 Jun 2020 07:59:05: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:59:12: 5000000 INFO @ Tue, 16 Jun 2020 07:59:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:19: 6000000 INFO @ Tue, 16 Jun 2020 07:59:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.10_summits.bed INFO @ Tue, 16 Jun 2020 07:59:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (333 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:59:26: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:59:33: 8000000 INFO @ Tue, 16 Jun 2020 07:59:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:59:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:59:36: #1 total tags in treatment: 8422562 INFO @ Tue, 16 Jun 2020 07:59:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:59:36: #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 07:59:36: #1 tags after filtering in treatment: 8422562 INFO @ Tue, 16 Jun 2020 07:59:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:59:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:59:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:59:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:59:37: #2 number of paired peaks: 299 WARNING @ Tue, 16 Jun 2020 07:59:37: Fewer paired peaks (299) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 299 pairs to build model! INFO @ Tue, 16 Jun 2020 07:59:37: start model_add_line... INFO @ Tue, 16 Jun 2020 07:59:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:59:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:59:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:59:37: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 07:59:37: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 07:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.20_model.r WARNING @ Tue, 16 Jun 2020 07:59:37: #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 07:59:37: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 07:59:37: #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 07:59:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:59:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228870/SRX2228870.20_summits.bed INFO @ Tue, 16 Jun 2020 08:00:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (141 records, 4 fields): 1 millis CompletedMACS2peakCalling