Job ID = 6453987 SRX = SRX1760695 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:56:04 prefetch.2.10.7: 1) Downloading 'SRR3503051'... 2020-06-21T08:56:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:29 prefetch.2.10.7: 'SRR3503051' is valid 2020-06-21T08:57:29 prefetch.2.10.7: 1) 'SRR3503051' was downloaded successfully 2020-06-21T08:57:29 prefetch.2.10.7: 'SRR3503051' has 0 unresolved dependencies Read 5078964 spots for SRR3503051/SRR3503051.sra Written 5078964 spots for SRR3503051/SRR3503051.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: 00:05:37 5078964 reads; of these: 5078964 (100.00%) were unpaired; of these: 1647701 (32.44%) aligned 0 times 2563278 (50.47%) aligned exactly 1 time 867985 (17.09%) aligned >1 times 67.56% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 166765 / 3431263 = 0.0486 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 18:06:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.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 18:06:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:30: 1000000 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 18:06:44: 2000000 INFO @ Sun, 21 Jun 2020 18:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.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 18:06:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:59: 3000000 INFO @ Sun, 21 Jun 2020 18:07:00: 1000000 INFO @ Sun, 21 Jun 2020 18:07:03: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:07:03: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:07:03: #1 total tags in treatment: 3264498 INFO @ Sun, 21 Jun 2020 18:07:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:03: #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 18:07:03: #1 tags after filtering in treatment: 3264238 INFO @ Sun, 21 Jun 2020 18:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:04: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 18:07:04: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:04: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:07:04: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:07:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.05_model.r WARNING @ Sun, 21 Jun 2020 18:07:04: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:07:04: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sun, 21 Jun 2020 18:07:04: #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 18:07:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:14: 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 18:07:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:15: Done! pass1 - making usageList (537 chroms): 2 millis pass2 - checking and writing primary data (1176 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.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 18:07:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:28: 3000000 INFO @ Sun, 21 Jun 2020 18:07:30: 1000000 INFO @ Sun, 21 Jun 2020 18:07:32: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:07:32: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:07:32: #1 total tags in treatment: 3264498 INFO @ Sun, 21 Jun 2020 18:07:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:32: #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 18:07:33: #1 tags after filtering in treatment: 3264238 INFO @ Sun, 21 Jun 2020 18:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:33: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 18:07:33: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:33: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:33: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:33: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:33: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:33: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:07:33: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.10_model.r WARNING @ Sun, 21 Jun 2020 18:07:33: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:07:33: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sun, 21 Jun 2020 18:07:33: #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 18:07:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:44: 2000000 INFO @ Sun, 21 Jun 2020 18:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:44: Done! pass1 - making usageList (428 chroms): 1 millis pass2 - checking and writing primary data (796 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:07:56: 3000000 INFO @ Sun, 21 Jun 2020 18:08:00: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:08:00: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:08:00: #1 total tags in treatment: 3264498 INFO @ Sun, 21 Jun 2020 18:08:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:00: #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 18:08:00: #1 tags after filtering in treatment: 3264238 INFO @ Sun, 21 Jun 2020 18:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:00: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:01: #2 number of paired peaks: 873 WARNING @ Sun, 21 Jun 2020 18:08:01: Fewer paired peaks (873) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 873 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:01: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:01: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:01: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:01: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:01: #2 predicted fragment length is 142 bps INFO @ Sun, 21 Jun 2020 18:08:01: #2 alternative fragment length(s) may be 142 bps INFO @ Sun, 21 Jun 2020 18:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.20_model.r WARNING @ Sun, 21 Jun 2020 18:08:01: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:08:01: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Sun, 21 Jun 2020 18:08:01: #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 18:08:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760695/SRX1760695.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:12: Done! pass1 - making usageList (300 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 17 millis CompletedMACS2peakCalling