Job ID = 6452517 SRX = SRX013114 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:28:19 prefetch.2.10.7: 1) Downloading 'SRR030380'... 2020-06-21T07:28:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:28:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:28:58 prefetch.2.10.7: 'SRR030380' is valid 2020-06-21T07:28:58 prefetch.2.10.7: 1) 'SRR030380' was downloaded successfully Read 2501288 spots for SRR030380/SRR030380.sra Written 2501288 spots for SRR030380/SRR030380.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:27 2501288 reads; of these: 2501288 (100.00%) were unpaired; of these: 767634 (30.69%) aligned 0 times 1471553 (58.83%) aligned exactly 1 time 262101 (10.48%) aligned >1 times 69.31% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 135541 / 1733654 = 0.0782 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 @ Sun, 21 Jun 2020 16:30:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:30:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:30:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:30:33: 1000000 INFO @ Sun, 21 Jun 2020 16:30:38: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:30:38: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:30:38: #1 total tags in treatment: 1598113 INFO @ Sun, 21 Jun 2020 16:30:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:30:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:30:38: #1 tags after filtering in treatment: 1597662 INFO @ Sun, 21 Jun 2020 16:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:30:38: #1 finished! INFO @ Sun, 21 Jun 2020 16:30:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:30:38: #2 number of paired peaks: 140 WARNING @ Sun, 21 Jun 2020 16:30:38: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 21 Jun 2020 16:30:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:30:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:30:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:30:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:30:38: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 16:30:38: #2 alternative fragment length(s) may be 38,106,468,500,586 bps INFO @ Sun, 21 Jun 2020 16:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.05_model.r WARNING @ Sun, 21 Jun 2020 16:30:38: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:30:38: #2 You may need to consider one of the other alternative d(s): 38,106,468,500,586 WARNING @ Sun, 21 Jun 2020 16:30:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:30:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:30:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:30:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:30:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:30:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.05_summits.bed INFO @ Sun, 21 Jun 2020 16:30:44: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 3 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 @ Sun, 21 Jun 2020 16:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:30:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:30:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:31:03: 1000000 INFO @ Sun, 21 Jun 2020 16:31:07: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:31:07: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:31:07: #1 total tags in treatment: 1598113 INFO @ Sun, 21 Jun 2020 16:31:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:31:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:31:07: #1 tags after filtering in treatment: 1597662 INFO @ Sun, 21 Jun 2020 16:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:31:07: #1 finished! INFO @ Sun, 21 Jun 2020 16:31:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:31:08: #2 number of paired peaks: 140 WARNING @ Sun, 21 Jun 2020 16:31:08: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 21 Jun 2020 16:31:08: start model_add_line... INFO @ Sun, 21 Jun 2020 16:31:08: start X-correlation... INFO @ Sun, 21 Jun 2020 16:31:08: end of X-cor INFO @ Sun, 21 Jun 2020 16:31:08: #2 finished! INFO @ Sun, 21 Jun 2020 16:31:08: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 16:31:08: #2 alternative fragment length(s) may be 38,106,468,500,586 bps INFO @ Sun, 21 Jun 2020 16:31:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.10_model.r WARNING @ Sun, 21 Jun 2020 16:31:08: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:31:08: #2 You may need to consider one of the other alternative d(s): 38,106,468,500,586 WARNING @ Sun, 21 Jun 2020 16:31:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:31:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:31:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:31:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:31:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:31:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:31:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.10_summits.bed INFO @ Sun, 21 Jun 2020 16:31:13: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 2 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 @ Sun, 21 Jun 2020 16:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:31:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:31:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:31:34: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:31:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:31:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:31:37: #1 total tags in treatment: 1598113 INFO @ Sun, 21 Jun 2020 16:31:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:31:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:31:38: #1 tags after filtering in treatment: 1597662 INFO @ Sun, 21 Jun 2020 16:31:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:31:38: #1 finished! INFO @ Sun, 21 Jun 2020 16:31:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:31:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:31:38: #2 number of paired peaks: 140 WARNING @ Sun, 21 Jun 2020 16:31:38: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 21 Jun 2020 16:31:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:31:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:31:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:31:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:31:38: #2 predicted fragment length is 38 bps INFO @ Sun, 21 Jun 2020 16:31:38: #2 alternative fragment length(s) may be 38,106,468,500,586 bps INFO @ Sun, 21 Jun 2020 16:31:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.20_model.r WARNING @ Sun, 21 Jun 2020 16:31:38: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:31:38: #2 You may need to consider one of the other alternative d(s): 38,106,468,500,586 WARNING @ Sun, 21 Jun 2020 16:31:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 16:31:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:31:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:31:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:31:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:31:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:31:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX013114/SRX013114.20_summits.bed INFO @ Sun, 21 Jun 2020 16:31:44: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (62 records, 4 fields): 2 millis CompletedMACS2peakCalling