Job ID = 6456512 SRX = SRX3511959 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:21:39 prefetch.2.10.7: 1) Downloading 'SRR6418944'... 2020-06-21T11:21:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:41 prefetch.2.10.7: 'SRR6418944' is valid 2020-06-21T11:22:41 prefetch.2.10.7: 1) 'SRR6418944' was downloaded successfully 2020-06-21T11:22:41 prefetch.2.10.7: 'SRR6418944' has 0 unresolved dependencies Read 3935133 spots for SRR6418944/SRR6418944.sra Written 3935133 spots for SRR6418944/SRR6418944.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: 00:01:55 3935133 reads; of these: 3935133 (100.00%) were unpaired; of these: 383221 (9.74%) aligned 0 times 2645372 (67.22%) aligned exactly 1 time 906540 (23.04%) aligned >1 times 90.26% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 316545 / 3551912 = 0.0891 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 20:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.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 20:26:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:26:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:26:49: 1000000 INFO @ Sun, 21 Jun 2020 20:26:56: 2000000 INFO @ Sun, 21 Jun 2020 20:27:03: 3000000 INFO @ Sun, 21 Jun 2020 20:27:05: #1 tag size is determined as 95 bps INFO @ Sun, 21 Jun 2020 20:27:05: #1 tag size = 95 INFO @ Sun, 21 Jun 2020 20:27:05: #1 total tags in treatment: 3235367 INFO @ Sun, 21 Jun 2020 20:27:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:05: #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 20:27:05: #1 tags after filtering in treatment: 3235331 INFO @ Sun, 21 Jun 2020 20:27:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:06: #2 number of paired peaks: 1286 INFO @ Sun, 21 Jun 2020 20:27:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:06: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 20:27:06: #2 alternative fragment length(s) may be 4,131 bps INFO @ Sun, 21 Jun 2020 20:27:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.05_model.r WARNING @ Sun, 21 Jun 2020 20:27:06: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:06: #2 You may need to consider one of the other alternative d(s): 4,131 WARNING @ Sun, 21 Jun 2020 20:27:06: #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 20:27:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:06: #3 Pre-compute pvalue-qvalue table... 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 20:27:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.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 20:27:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.05_summits.bed INFO @ Sun, 21 Jun 2020 20:27:16: Done! pass1 - making usageList (299 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:19: 1000000 INFO @ Sun, 21 Jun 2020 20:27:26: 2000000 INFO @ Sun, 21 Jun 2020 20:27:34: 3000000 INFO @ Sun, 21 Jun 2020 20:27:36: #1 tag size is determined as 95 bps INFO @ Sun, 21 Jun 2020 20:27:36: #1 tag size = 95 INFO @ Sun, 21 Jun 2020 20:27:36: #1 total tags in treatment: 3235367 INFO @ Sun, 21 Jun 2020 20:27:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:36: #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 20:27:36: #1 tags after filtering in treatment: 3235331 INFO @ Sun, 21 Jun 2020 20:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:36: #2 number of paired peaks: 1286 INFO @ Sun, 21 Jun 2020 20:27:36: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:36: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:36: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:36: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:36: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 20:27:36: #2 alternative fragment length(s) may be 4,131 bps INFO @ Sun, 21 Jun 2020 20:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.10_model.r WARNING @ Sun, 21 Jun 2020 20:27:36: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:27:36: #2 You may need to consider one of the other alternative d(s): 4,131 WARNING @ Sun, 21 Jun 2020 20:27:36: #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 20:27:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:36: #3 Pre-compute pvalue-qvalue table... 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 20:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.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 20:27:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:27:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:27:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.10_summits.bed INFO @ Sun, 21 Jun 2020 20:27:47: Done! pass1 - making usageList (181 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:50: 1000000 INFO @ Sun, 21 Jun 2020 20:27:59: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:28:09: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:28:11: #1 tag size is determined as 95 bps INFO @ Sun, 21 Jun 2020 20:28:11: #1 tag size = 95 INFO @ Sun, 21 Jun 2020 20:28:11: #1 total tags in treatment: 3235367 INFO @ Sun, 21 Jun 2020 20:28:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:28:11: #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 20:28:12: #1 tags after filtering in treatment: 3235331 INFO @ Sun, 21 Jun 2020 20:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:28:12: #1 finished! INFO @ Sun, 21 Jun 2020 20:28:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:28:12: #2 number of paired peaks: 1286 INFO @ Sun, 21 Jun 2020 20:28:12: start model_add_line... INFO @ Sun, 21 Jun 2020 20:28:12: start X-correlation... INFO @ Sun, 21 Jun 2020 20:28:12: end of X-cor INFO @ Sun, 21 Jun 2020 20:28:12: #2 finished! INFO @ Sun, 21 Jun 2020 20:28:12: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 20:28:12: #2 alternative fragment length(s) may be 4,131 bps INFO @ Sun, 21 Jun 2020 20:28:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.20_model.r WARNING @ Sun, 21 Jun 2020 20:28:12: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:28:12: #2 You may need to consider one of the other alternative d(s): 4,131 WARNING @ Sun, 21 Jun 2020 20:28:12: #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 20:28:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:28:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:28:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511959/SRX3511959.20_summits.bed INFO @ Sun, 21 Jun 2020 20:28:23: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 3 millis CompletedMACS2peakCalling