Job ID = 6456349 SRX = SRX3380796 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:46:38 prefetch.2.10.7: 1) Downloading 'SRR6278159'... 2020-06-21T10:46:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:47:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:47:31 prefetch.2.10.7: 'SRR6278159' is valid 2020-06-21T10:47:31 prefetch.2.10.7: 1) 'SRR6278159' was downloaded successfully Read 8212441 spots for SRR6278159/SRR6278159.sra Written 8212441 spots for SRR6278159/SRR6278159.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: 00:02:20 8212441 reads; of these: 8212441 (100.00%) were unpaired; of these: 306560 (3.73%) aligned 0 times 6334078 (77.13%) aligned exactly 1 time 1571803 (19.14%) aligned >1 times 96.27% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 798729 / 7905881 = 0.1010 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 19:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.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 19:52:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:34: 1000000 INFO @ Sun, 21 Jun 2020 19:52:39: 2000000 INFO @ Sun, 21 Jun 2020 19:52:44: 3000000 INFO @ Sun, 21 Jun 2020 19:52:49: 4000000 INFO @ Sun, 21 Jun 2020 19:52:54: 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 19:52:59: 6000000 INFO @ Sun, 21 Jun 2020 19:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.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 19:52:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:04: 7000000 INFO @ Sun, 21 Jun 2020 19:53:04: 1000000 INFO @ Sun, 21 Jun 2020 19:53:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:53:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:53:05: #1 total tags in treatment: 7107152 INFO @ Sun, 21 Jun 2020 19:53:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:05: #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 19:53:05: #1 tags after filtering in treatment: 7107109 INFO @ Sun, 21 Jun 2020 19:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:05: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:06: #2 number of paired peaks: 292 WARNING @ Sun, 21 Jun 2020 19:53:06: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:06: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 19:53:06: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 21 Jun 2020 19:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.05_model.r WARNING @ Sun, 21 Jun 2020 19:53:06: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:06: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 21 Jun 2020 19:53:06: #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 19:53:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:09: 2000000 INFO @ Sun, 21 Jun 2020 19:53:15: 3000000 INFO @ Sun, 21 Jun 2020 19:53:20: 4000000 INFO @ Sun, 21 Jun 2020 19:53:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:25: 5000000 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 19:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.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 19:53:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:30: 6000000 INFO @ Sun, 21 Jun 2020 19:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.05_summits.bed INFO @ Sun, 21 Jun 2020 19:53:30: Done! pass1 - making usageList (315 chroms): 1 millis pass2 - checking and writing primary data (971 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:35: 1000000 INFO @ Sun, 21 Jun 2020 19:53:35: 7000000 INFO @ Sun, 21 Jun 2020 19:53:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:53:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:53:36: #1 total tags in treatment: 7107152 INFO @ Sun, 21 Jun 2020 19:53:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:36: #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 19:53:37: #1 tags after filtering in treatment: 7107109 INFO @ Sun, 21 Jun 2020 19:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:37: #2 number of paired peaks: 292 WARNING @ Sun, 21 Jun 2020 19:53:37: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:37: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 19:53:37: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 21 Jun 2020 19:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.10_model.r WARNING @ Sun, 21 Jun 2020 19:53:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:37: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 21 Jun 2020 19:53:37: #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 19:53:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:40: 2000000 INFO @ Sun, 21 Jun 2020 19:53:46: 3000000 INFO @ Sun, 21 Jun 2020 19:53:51: 4000000 INFO @ Sun, 21 Jun 2020 19:53:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:56: 5000000 INFO @ Sun, 21 Jun 2020 19:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:01: Done! pass1 - making usageList (176 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:02: 6000000 INFO @ Sun, 21 Jun 2020 19:54:07: 7000000 INFO @ Sun, 21 Jun 2020 19:54:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:54:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:54:08: #1 total tags in treatment: 7107152 INFO @ Sun, 21 Jun 2020 19:54:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:54:08: #1 tags after filtering in treatment: 7107109 INFO @ Sun, 21 Jun 2020 19:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:09: #2 number of paired peaks: 292 WARNING @ Sun, 21 Jun 2020 19:54:09: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Sun, 21 Jun 2020 19:54:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:09: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 19:54:09: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 21 Jun 2020 19:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.20_model.r WARNING @ Sun, 21 Jun 2020 19:54:09: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:09: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 21 Jun 2020 19:54:09: #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 19:54:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380796/SRX3380796.20_summits.bed INFO @ Sun, 21 Jun 2020 19:54:33: Done! pass1 - making usageList (99 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 4 millis CompletedMACS2peakCalling