Job ID = 6366010 SRX = SRX044023 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:29 prefetch.2.10.7: 1) Downloading 'SRR107605'... 2020-06-15T23:44:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:08 prefetch.2.10.7: 'SRR107605' is valid 2020-06-15T23:46:08 prefetch.2.10.7: 1) 'SRR107605' was downloaded successfully Read 12769350 spots for SRR107605/SRR107605.sra Written 12769350 spots for SRR107605/SRR107605.sra 2020-06-15T23:47:00 prefetch.2.10.7: 1) Downloading 'SRR107606'... 2020-06-15T23:47:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:27 prefetch.2.10.7: 'SRR107606' is valid 2020-06-15T23:50:27 prefetch.2.10.7: 1) 'SRR107606' was downloaded successfully Read 16223713 spots for SRR107606/SRR107606.sra Written 16223713 spots for SRR107606/SRR107606.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: 00:01:33 28993063 reads; of these: 28993063 (100.00%) were unpaired; of these: 27798276 (95.88%) aligned 0 times 1014360 (3.50%) aligned exactly 1 time 180427 (0.62%) aligned >1 times 4.12% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 34821 / 1194787 = 0.0291 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 08:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.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 08:54:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:07: 1000000 INFO @ Tue, 16 Jun 2020 08:54:08: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 08:54:08: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 08:54:08: #1 total tags in treatment: 1159966 INFO @ Tue, 16 Jun 2020 08:54:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:08: #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 08:54:08: #1 tags after filtering in treatment: 1159966 INFO @ Tue, 16 Jun 2020 08:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:54:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:08: #2 number of paired peaks: 304 WARNING @ Tue, 16 Jun 2020 08:54:08: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:08: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:54:08: #2 alternative fragment length(s) may be 35,96,547 bps INFO @ Tue, 16 Jun 2020 08:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.05_model.r WARNING @ Tue, 16 Jun 2020 08:54:08: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:54:08: #2 You may need to consider one of the other alternative d(s): 35,96,547 WARNING @ Tue, 16 Jun 2020 08:54:08: #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 08:54:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.05_summits.bed INFO @ Tue, 16 Jun 2020 08:54:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 4 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 08:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.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 08:54:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:37: 1000000 INFO @ Tue, 16 Jun 2020 08:54:38: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 08:54:38: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 08:54:38: #1 total tags in treatment: 1159966 INFO @ Tue, 16 Jun 2020 08:54:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:38: #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 08:54:38: #1 tags after filtering in treatment: 1159966 INFO @ Tue, 16 Jun 2020 08:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:54:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:38: #2 number of paired peaks: 304 WARNING @ Tue, 16 Jun 2020 08:54:38: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:38: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:54:38: #2 alternative fragment length(s) may be 35,96,547 bps INFO @ Tue, 16 Jun 2020 08:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.10_model.r WARNING @ Tue, 16 Jun 2020 08:54:38: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:54:38: #2 You may need to consider one of the other alternative d(s): 35,96,547 WARNING @ Tue, 16 Jun 2020 08:54:38: #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 08:54:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.10_summits.bed INFO @ Tue, 16 Jun 2020 08:54:41: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (37 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 08:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.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 08:55:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:01: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:55:07: 1000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:55:08: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 08:55:08: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 08:55:08: #1 total tags in treatment: 1159966 INFO @ Tue, 16 Jun 2020 08:55:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:55:08: #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 08:55:08: #1 tags after filtering in treatment: 1159966 INFO @ Tue, 16 Jun 2020 08:55:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:55:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:55:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:55:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:55:08: #2 number of paired peaks: 304 WARNING @ Tue, 16 Jun 2020 08:55:08: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 16 Jun 2020 08:55:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:55:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:55:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:55:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:55:08: #2 predicted fragment length is 35 bps INFO @ Tue, 16 Jun 2020 08:55:08: #2 alternative fragment length(s) may be 35,96,547 bps INFO @ Tue, 16 Jun 2020 08:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.20_model.r WARNING @ Tue, 16 Jun 2020 08:55:08: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:55:08: #2 You may need to consider one of the other alternative d(s): 35,96,547 WARNING @ Tue, 16 Jun 2020 08:55:08: #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 08:55:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:55:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:55:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:55:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX044023/SRX044023.20_summits.bed INFO @ Tue, 16 Jun 2020 08:55:11: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling