Job ID = 6454005 SRX = SRX1760709 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:00:34 prefetch.2.10.7: 1) Downloading 'SRR3503072'... 2020-06-21T09:00:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:38 prefetch.2.10.7: 'SRR3503072' is valid 2020-06-21T09:02:38 prefetch.2.10.7: 1) 'SRR3503072' was downloaded successfully 2020-06-21T09:02:38 prefetch.2.10.7: 'SRR3503072' has 0 unresolved dependencies Read 5615224 spots for SRR3503072/SRR3503072.sra Written 5615224 spots for SRR3503072/SRR3503072.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: 00:05:11 5615224 reads; of these: 5615224 (100.00%) were unpaired; of these: 1170516 (20.85%) aligned 0 times 3290423 (58.60%) aligned exactly 1 time 1154285 (20.56%) aligned >1 times 79.15% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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] 213786 / 4444708 = 0.0481 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 18:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.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 18:11:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:20: 1000000 INFO @ Sun, 21 Jun 2020 18:11:31: 2000000 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 18:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.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 18:11:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:43: 3000000 INFO @ Sun, 21 Jun 2020 18:11:49: 1000000 INFO @ Sun, 21 Jun 2020 18:11:56: 4000000 INFO @ Sun, 21 Jun 2020 18:11:59: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:11:59: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:11:59: #1 total tags in treatment: 4230922 INFO @ Sun, 21 Jun 2020 18:11:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:59: #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 18:11:59: #1 tags after filtering in treatment: 4230702 INFO @ Sun, 21 Jun 2020 18:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:59: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:59: #2 number of paired peaks: 1014 INFO @ Sun, 21 Jun 2020 18:11:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:59: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:11:59: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.05_model.r WARNING @ Sun, 21 Jun 2020 18:11:59: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:11:59: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sun, 21 Jun 2020 18:11:59: #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 18:11:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:00: 2000000 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 18:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.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 18:12:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:12:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:12:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:12:10: 3000000 INFO @ Sun, 21 Jun 2020 18:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.05_summits.bed INFO @ Sun, 21 Jun 2020 18:12:15: Done! pass1 - making usageList (557 chroms): 2 millis pass2 - checking and writing primary data (1296 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:12:19: 1000000 INFO @ Sun, 21 Jun 2020 18:12:21: 4000000 INFO @ Sun, 21 Jun 2020 18:12:24: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:12:24: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:12:24: #1 total tags in treatment: 4230922 INFO @ Sun, 21 Jun 2020 18:12:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:24: #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 18:12:24: #1 tags after filtering in treatment: 4230702 INFO @ Sun, 21 Jun 2020 18:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:25: #2 number of paired peaks: 1014 INFO @ Sun, 21 Jun 2020 18:12:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:25: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:12:25: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:12:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.10_model.r WARNING @ Sun, 21 Jun 2020 18:12:25: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:25: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sun, 21 Jun 2020 18:12:25: #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 18:12:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:29: 2000000 INFO @ Sun, 21 Jun 2020 18:12:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:12:39: 3000000 INFO @ Sun, 21 Jun 2020 18:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.10_summits.bed INFO @ Sun, 21 Jun 2020 18:12:41: Done! pass1 - making usageList (503 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:12:49: 4000000 INFO @ Sun, 21 Jun 2020 18:12:51: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:12:51: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:12:51: #1 total tags in treatment: 4230922 INFO @ Sun, 21 Jun 2020 18:12:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:51: #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 18:12:51: #1 tags after filtering in treatment: 4230702 INFO @ Sun, 21 Jun 2020 18:12:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:52: #2 number of paired peaks: 1014 INFO @ Sun, 21 Jun 2020 18:12:52: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:12:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:52: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:12:52: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:12:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.20_model.r WARNING @ Sun, 21 Jun 2020 18:12:52: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:52: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sun, 21 Jun 2020 18:12:52: #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 18:12:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760709/SRX1760709.20_summits.bed INFO @ Sun, 21 Jun 2020 18:13:07: Done! pass1 - making usageList (383 chroms): 1 millis pass2 - checking and writing primary data (646 records, 4 fields): 12 millis CompletedMACS2peakCalling