Job ID = 6457901 SRX = SRX485207 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:59:18 prefetch.2.10.7: 1) Downloading 'SRR1187965'... 2020-06-21T11:59:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:03:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:03:49 prefetch.2.10.7: 1) 'SRR1187965' was downloaded successfully 2020-06-21T12:03:49 prefetch.2.10.7: 'SRR1187965' has 0 unresolved dependencies Read 27157073 spots for SRR1187965/SRR1187965.sra Written 27157073 spots for SRR1187965/SRR1187965.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: 00:07:14 27157073 reads; of these: 27157073 (100.00%) were unpaired; of these: 2770414 (10.20%) aligned 0 times 16933570 (62.35%) aligned exactly 1 time 7453089 (27.44%) aligned >1 times 89.80% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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_sort_core] merging from 12 files... [bam_rmdupse_core] 15234592 / 24386659 = 0.6247 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 21:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.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 21:17:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:31: 1000000 INFO @ Sun, 21 Jun 2020 21:17:36: 2000000 INFO @ Sun, 21 Jun 2020 21:17:42: 3000000 INFO @ Sun, 21 Jun 2020 21:17:47: 4000000 INFO @ Sun, 21 Jun 2020 21:17:52: 5000000 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 21:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.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 21:17:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:17:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:17:58: 6000000 INFO @ Sun, 21 Jun 2020 21:18:01: 1000000 INFO @ Sun, 21 Jun 2020 21:18:04: 7000000 INFO @ Sun, 21 Jun 2020 21:18:07: 2000000 INFO @ Sun, 21 Jun 2020 21:18:10: 8000000 INFO @ Sun, 21 Jun 2020 21:18:13: 3000000 INFO @ Sun, 21 Jun 2020 21:18:16: 9000000 INFO @ Sun, 21 Jun 2020 21:18:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:18:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:18:17: #1 total tags in treatment: 9152067 INFO @ Sun, 21 Jun 2020 21:18:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:17: #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 21:18:17: #1 tags after filtering in treatment: 9152015 INFO @ Sun, 21 Jun 2020 21:18:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:18:18: #2 number of paired peaks: 2707 INFO @ Sun, 21 Jun 2020 21:18:18: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:18: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:18: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:18: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:18: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 21:18:18: #2 alternative fragment length(s) may be 3,69 bps INFO @ Sun, 21 Jun 2020 21:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.05_model.r WARNING @ Sun, 21 Jun 2020 21:18:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:18:18: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Sun, 21 Jun 2020 21:18:18: #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 21:18:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:18:19: 4000000 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 21:18:25: 5000000 INFO @ Sun, 21 Jun 2020 21:18:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.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 21:18:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:30: 6000000 INFO @ Sun, 21 Jun 2020 21:18:31: 1000000 INFO @ Sun, 21 Jun 2020 21:18:37: 7000000 INFO @ Sun, 21 Jun 2020 21:18:38: 2000000 INFO @ Sun, 21 Jun 2020 21:18:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:18:43: 8000000 INFO @ Sun, 21 Jun 2020 21:18:44: 3000000 INFO @ Sun, 21 Jun 2020 21:18:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:18:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:18:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.05_summits.bed INFO @ Sun, 21 Jun 2020 21:18:49: Done! pass1 - making usageList (779 chroms): 2 millis pass2 - checking and writing primary data (3942 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:18:49: 9000000 INFO @ Sun, 21 Jun 2020 21:18:50: 4000000 INFO @ Sun, 21 Jun 2020 21:18:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:18:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:18:50: #1 total tags in treatment: 9152067 INFO @ Sun, 21 Jun 2020 21:18:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:18:50: #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 21:18:50: #1 tags after filtering in treatment: 9152015 INFO @ Sun, 21 Jun 2020 21:18:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:18:50: #1 finished! INFO @ Sun, 21 Jun 2020 21:18:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:18:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:18:51: #2 number of paired peaks: 2707 INFO @ Sun, 21 Jun 2020 21:18:51: start model_add_line... INFO @ Sun, 21 Jun 2020 21:18:51: start X-correlation... INFO @ Sun, 21 Jun 2020 21:18:51: end of X-cor INFO @ Sun, 21 Jun 2020 21:18:51: #2 finished! INFO @ Sun, 21 Jun 2020 21:18:51: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 21:18:51: #2 alternative fragment length(s) may be 3,69 bps INFO @ Sun, 21 Jun 2020 21:18:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.10_model.r WARNING @ Sun, 21 Jun 2020 21:18:51: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:18:51: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Sun, 21 Jun 2020 21:18:51: #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 21:18:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:18:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:18:55: 5000000 INFO @ Sun, 21 Jun 2020 21:19:01: 6000000 INFO @ Sun, 21 Jun 2020 21:19:07: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:19:12: 8000000 INFO @ Sun, 21 Jun 2020 21:19:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:19:18: 9000000 INFO @ Sun, 21 Jun 2020 21:19:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:19:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:19:19: #1 total tags in treatment: 9152067 INFO @ Sun, 21 Jun 2020 21:19:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:19:19: #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 21:19:19: #1 tags after filtering in treatment: 9152015 INFO @ Sun, 21 Jun 2020 21:19:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:19:19: #1 finished! INFO @ Sun, 21 Jun 2020 21:19:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:19:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:19:20: #2 number of paired peaks: 2707 INFO @ Sun, 21 Jun 2020 21:19:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:19:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:19:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:19:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:19:20: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 21:19:20: #2 alternative fragment length(s) may be 3,69 bps INFO @ Sun, 21 Jun 2020 21:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.20_model.r WARNING @ Sun, 21 Jun 2020 21:19:20: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:19:20: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Sun, 21 Jun 2020 21:19:20: #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 21:19:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.10_summits.bed INFO @ Sun, 21 Jun 2020 21:19:24: Done! pass1 - making usageList (639 chroms): 2 millis pass2 - checking and writing primary data (2598 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:19:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:19:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:19:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:19:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX485207/SRX485207.20_summits.bed INFO @ Sun, 21 Jun 2020 21:19:52: Done! pass1 - making usageList (473 chroms): 1 millis pass2 - checking and writing primary data (1233 records, 4 fields): 15 millis CompletedMACS2peakCalling