Job ID = 6455291 SRX = SRX287668 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:57:40 prefetch.2.10.7: 1) Downloading 'SRR869856'... 2020-06-21T09:57:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:58:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:58:39 prefetch.2.10.7: 'SRR869856' is valid 2020-06-21T09:58:39 prefetch.2.10.7: 1) 'SRR869856' was downloaded successfully Read 7840701 spots for SRR869856/SRR869856.sra Written 7840701 spots for SRR869856/SRR869856.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: 00:02:33 7840701 reads; of these: 7840701 (100.00%) were unpaired; of these: 384964 (4.91%) aligned 0 times 5205076 (66.39%) aligned exactly 1 time 2250661 (28.70%) aligned >1 times 95.09% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 1241258 / 7455737 = 0.1665 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 19:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.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 19:04:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:07: 1000000 INFO @ Sun, 21 Jun 2020 19:04:13: 2000000 INFO @ Sun, 21 Jun 2020 19:04:19: 3000000 INFO @ Sun, 21 Jun 2020 19:04:25: 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 19:04:31: 5000000 INFO @ Sun, 21 Jun 2020 19:04:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.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 19:04:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:04:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:04:37: 6000000 INFO @ Sun, 21 Jun 2020 19:04:38: 1000000 INFO @ Sun, 21 Jun 2020 19:04:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:39: #1 total tags in treatment: 6214479 INFO @ Sun, 21 Jun 2020 19:04:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:39: #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 19:04:39: #1 tags after filtering in treatment: 6214473 INFO @ Sun, 21 Jun 2020 19:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:40: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 19:04:40: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:40: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:04:40: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 21 Jun 2020 19:04:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.05_model.r WARNING @ Sun, 21 Jun 2020 19:04:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:40: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 21 Jun 2020 19:04:40: #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 19:04:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:44: 2000000 INFO @ Sun, 21 Jun 2020 19:04:50: 3000000 INFO @ Sun, 21 Jun 2020 19:04:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:56: 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 19:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.05_summits.bed INFO @ Sun, 21 Jun 2020 19:05:01: Done! pass1 - making usageList (531 chroms): 1 millis pass2 - checking and writing primary data (2031 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.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 19:05:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:05:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:05:03: 5000000 INFO @ Sun, 21 Jun 2020 19:05:09: 1000000 INFO @ Sun, 21 Jun 2020 19:05:09: 6000000 INFO @ Sun, 21 Jun 2020 19:05:11: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:11: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:11: #1 total tags in treatment: 6214479 INFO @ Sun, 21 Jun 2020 19:05:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:11: #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 19:05:11: #1 tags after filtering in treatment: 6214473 INFO @ Sun, 21 Jun 2020 19:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:12: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 19:05:12: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:12: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:05:12: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 21 Jun 2020 19:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.10_model.r WARNING @ Sun, 21 Jun 2020 19:05:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:12: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 21 Jun 2020 19:05:12: #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 19:05:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:15: 2000000 INFO @ Sun, 21 Jun 2020 19:05:20: 3000000 INFO @ Sun, 21 Jun 2020 19:05:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:26: 4000000 INFO @ Sun, 21 Jun 2020 19:05:33: 5000000 INFO @ Sun, 21 Jun 2020 19:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:33: Done! pass1 - making usageList (426 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:05:38: 6000000 INFO @ Sun, 21 Jun 2020 19:05:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:05:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:05:40: #1 total tags in treatment: 6214479 INFO @ Sun, 21 Jun 2020 19:05:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:05:40: #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 19:05:40: #1 tags after filtering in treatment: 6214473 INFO @ Sun, 21 Jun 2020 19:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:05:40: #1 finished! INFO @ Sun, 21 Jun 2020 19:05:40: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:05:41: #2 number of paired peaks: 774 WARNING @ Sun, 21 Jun 2020 19:05:41: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Sun, 21 Jun 2020 19:05:41: start model_add_line... INFO @ Sun, 21 Jun 2020 19:05:41: start X-correlation... INFO @ Sun, 21 Jun 2020 19:05:41: end of X-cor INFO @ Sun, 21 Jun 2020 19:05:41: #2 finished! INFO @ Sun, 21 Jun 2020 19:05:41: #2 predicted fragment length is 48 bps INFO @ Sun, 21 Jun 2020 19:05:41: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 21 Jun 2020 19:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.20_model.r WARNING @ Sun, 21 Jun 2020 19:05:41: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:05:41: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 21 Jun 2020 19:05:41: #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 19:05:41: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:05:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:06:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:06:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:06:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287668/SRX287668.20_summits.bed INFO @ Sun, 21 Jun 2020 19:06:02: Done! pass1 - making usageList (187 chroms): 2 millis pass2 - checking and writing primary data (362 records, 4 fields): 7 millis CompletedMACS2peakCalling