Job ID = 6458452 SRX = SRX5227006 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:37 prefetch.2.10.7: 1) Downloading 'SRR8417921'... 2020-06-21T12:30:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:33:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:33:17 prefetch.2.10.7: 'SRR8417921' is valid 2020-06-21T12:33:17 prefetch.2.10.7: 1) 'SRR8417921' was downloaded successfully 2020-06-21T12:33:17 prefetch.2.10.7: 'SRR8417921' has 0 unresolved dependencies Read 8837846 spots for SRR8417921/SRR8417921.sra Written 8837846 spots for SRR8417921/SRR8417921.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: 00:03:42 8837846 reads; of these: 8837846 (100.00%) were unpaired; of these: 1972665 (22.32%) aligned 0 times 4759551 (53.85%) aligned exactly 1 time 2105630 (23.83%) aligned >1 times 77.68% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 798681 / 6865181 = 0.1163 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 21:41:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.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 21:41:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:12: 1000000 INFO @ Sun, 21 Jun 2020 21:41:17: 2000000 INFO @ Sun, 21 Jun 2020 21:41:23: 3000000 INFO @ Sun, 21 Jun 2020 21:41:29: 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 @ Sun, 21 Jun 2020 21:41:35: 5000000 INFO @ Sun, 21 Jun 2020 21:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.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 21:41:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:41:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:41:41: 6000000 INFO @ Sun, 21 Jun 2020 21:41:42: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 21:41:42: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 21:41:42: #1 total tags in treatment: 6066500 INFO @ Sun, 21 Jun 2020 21:41:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:41:42: #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 21:41:42: 1000000 INFO @ Sun, 21 Jun 2020 21:41:42: #1 tags after filtering in treatment: 6066367 INFO @ Sun, 21 Jun 2020 21:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:41:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:41:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:41:43: #2 number of paired peaks: 1466 INFO @ Sun, 21 Jun 2020 21:41:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:41:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:41:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:41:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:41:43: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:41:43: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 21:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.05_model.r WARNING @ Sun, 21 Jun 2020 21:41:43: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:41:43: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 21:41:43: #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 21:41:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:41:47: 2000000 INFO @ Sun, 21 Jun 2020 21:41:53: 3000000 INFO @ Sun, 21 Jun 2020 21:41:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:41:59: 4000000 INFO @ Sun, 21 Jun 2020 21:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.05_summits.bed INFO @ Sun, 21 Jun 2020 21:42:02: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2514 records, 4 fields): 33 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 21:42:05: 5000000 INFO @ Sun, 21 Jun 2020 21:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.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 21:42:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:42:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:42:11: 6000000 INFO @ Sun, 21 Jun 2020 21:42:12: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 21:42:12: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 21:42:12: #1 total tags in treatment: 6066500 INFO @ Sun, 21 Jun 2020 21:42:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:12: #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 21:42:12: 1000000 INFO @ Sun, 21 Jun 2020 21:42:13: #1 tags after filtering in treatment: 6066367 INFO @ Sun, 21 Jun 2020 21:42:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:13: #2 number of paired peaks: 1466 INFO @ Sun, 21 Jun 2020 21:42:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:13: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:42:13: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 21:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.10_model.r WARNING @ Sun, 21 Jun 2020 21:42:13: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:42:13: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 21:42:13: #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 21:42:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:42:18: 2000000 INFO @ Sun, 21 Jun 2020 21:42:23: 3000000 INFO @ Sun, 21 Jun 2020 21:42:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:42:29: 4000000 INFO @ Sun, 21 Jun 2020 21:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.10_summits.bed INFO @ Sun, 21 Jun 2020 21:42:33: Done! pass1 - making usageList (349 chroms): 2 millis pass2 - checking and writing primary data (1109 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:42:35: 5000000 INFO @ Sun, 21 Jun 2020 21:42:41: 6000000 INFO @ Sun, 21 Jun 2020 21:42:41: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 21:42:41: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 21:42:41: #1 total tags in treatment: 6066500 INFO @ Sun, 21 Jun 2020 21:42:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:42:41: #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 21:42:42: #1 tags after filtering in treatment: 6066367 INFO @ Sun, 21 Jun 2020 21:42:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:42:42: #1 finished! INFO @ Sun, 21 Jun 2020 21:42:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:42:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:42:43: #2 number of paired peaks: 1466 INFO @ Sun, 21 Jun 2020 21:42:43: start model_add_line... INFO @ Sun, 21 Jun 2020 21:42:43: start X-correlation... INFO @ Sun, 21 Jun 2020 21:42:43: end of X-cor INFO @ Sun, 21 Jun 2020 21:42:43: #2 finished! INFO @ Sun, 21 Jun 2020 21:42:43: #2 predicted fragment length is 102 bps INFO @ Sun, 21 Jun 2020 21:42:43: #2 alternative fragment length(s) may be 102 bps INFO @ Sun, 21 Jun 2020 21:42:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.20_model.r WARNING @ Sun, 21 Jun 2020 21:42:43: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:42:43: #2 You may need to consider one of the other alternative d(s): 102 WARNING @ Sun, 21 Jun 2020 21:42:43: #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 21:42:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:42:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:42:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:43:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:43:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5227006/SRX5227006.20_summits.bed INFO @ Sun, 21 Jun 2020 21:43:03: Done! BigWig に変換しました。 pass1 - making usageList (174 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 11 millis CompletedMACS2peakCalling