Job ID = 6366783 SRX = SRX233448 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:01 prefetch.2.10.7: 1) Downloading 'SRR701503'... 2020-06-15T23:12:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:28 prefetch.2.10.7: 'SRR701503' is valid 2020-06-15T23:12:28 prefetch.2.10.7: 1) 'SRR701503' was downloaded successfully Read 5535812 spots for SRR701503/SRR701503.sra Written 5535812 spots for SRR701503/SRR701503.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 5535812 reads; of these: 5535812 (100.00%) were unpaired; of these: 1787643 (32.29%) aligned 0 times 3141150 (56.74%) aligned exactly 1 time 607019 (10.97%) aligned >1 times 67.71% 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] 190787 / 3748169 = 0.0509 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 08:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.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 08:14:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:59: 1000000 INFO @ Tue, 16 Jun 2020 08:15:03: 2000000 INFO @ Tue, 16 Jun 2020 08:15:08: 3000000 INFO @ Tue, 16 Jun 2020 08:15:10: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:10: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:10: #1 total tags in treatment: 3557382 INFO @ Tue, 16 Jun 2020 08:15:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:10: #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 08:15:10: #1 tags after filtering in treatment: 3557382 INFO @ Tue, 16 Jun 2020 08:15:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:11: #2 number of paired peaks: 402 WARNING @ Tue, 16 Jun 2020 08:15:11: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:11: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:11: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:15:11: #2 alternative fragment length(s) may be 4,34,444,576 bps INFO @ Tue, 16 Jun 2020 08:15:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.05_model.r WARNING @ Tue, 16 Jun 2020 08:15:11: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:11: #2 You may need to consider one of the other alternative d(s): 4,34,444,576 WARNING @ Tue, 16 Jun 2020 08:15:11: #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 08:15:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 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 08:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.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 08:15:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:29: 1000000 INFO @ Tue, 16 Jun 2020 08:15:35: 2000000 INFO @ Tue, 16 Jun 2020 08:15:40: 3000000 INFO @ Tue, 16 Jun 2020 08:15:43: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:15:43: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:15:43: #1 total tags in treatment: 3557382 INFO @ Tue, 16 Jun 2020 08:15:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:43: #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 08:15:43: #1 tags after filtering in treatment: 3557382 INFO @ Tue, 16 Jun 2020 08:15:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:43: #2 number of paired peaks: 402 WARNING @ Tue, 16 Jun 2020 08:15:43: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:43: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:15:43: #2 alternative fragment length(s) may be 4,34,444,576 bps INFO @ Tue, 16 Jun 2020 08:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.10_model.r WARNING @ Tue, 16 Jun 2020 08:15:43: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:15:43: #2 You may need to consider one of the other alternative d(s): 4,34,444,576 WARNING @ Tue, 16 Jun 2020 08:15:43: #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 08:15:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:50: #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 08:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.10_summits.bed INFO @ Tue, 16 Jun 2020 08:15:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.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 08:15:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:59: 1000000 INFO @ Tue, 16 Jun 2020 08:16:05: 2000000 INFO @ Tue, 16 Jun 2020 08:16:10: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:13: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:16:13: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:16:13: #1 total tags in treatment: 3557382 INFO @ Tue, 16 Jun 2020 08:16:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:13: #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 08:16:13: #1 tags after filtering in treatment: 3557382 INFO @ Tue, 16 Jun 2020 08:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:13: #2 number of paired peaks: 402 WARNING @ Tue, 16 Jun 2020 08:16:13: Fewer paired peaks (402) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 402 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:13: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 08:16:13: #2 alternative fragment length(s) may be 4,34,444,576 bps INFO @ Tue, 16 Jun 2020 08:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.20_model.r WARNING @ Tue, 16 Jun 2020 08:16:13: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:13: #2 You may need to consider one of the other alternative d(s): 4,34,444,576 WARNING @ Tue, 16 Jun 2020 08:16:13: #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 08:16:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX233448/SRX233448.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (41 records, 4 fields): 1 millis CompletedMACS2peakCalling