Job ID = 6459614 SRX = SRX7299239 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:22:34 prefetch.2.10.7: 1) Downloading 'SRR10620139'... 2020-06-21T13:22:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:24:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:24:24 prefetch.2.10.7: 'SRR10620139' is valid 2020-06-21T13:24:24 prefetch.2.10.7: 1) 'SRR10620139' was downloaded successfully Read 15424468 spots for SRR10620139/SRR10620139.sra Written 15424468 spots for SRR10620139/SRR10620139.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: 00:03:44 15424468 reads; of these: 15424468 (100.00%) were unpaired; of these: 861500 (5.59%) aligned 0 times 10768051 (69.81%) aligned exactly 1 time 3794917 (24.60%) aligned >1 times 94.41% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 2144447 / 14562968 = 0.1473 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 22:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.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 22:32:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:32:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:32:40: 1000000 INFO @ Sun, 21 Jun 2020 22:32:46: 2000000 INFO @ Sun, 21 Jun 2020 22:32:51: 3000000 INFO @ Sun, 21 Jun 2020 22:32:57: 4000000 INFO @ Sun, 21 Jun 2020 22:33:02: 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 22:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.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 22:33:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:33:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:33:08: 6000000 INFO @ Sun, 21 Jun 2020 22:33:11: 1000000 INFO @ Sun, 21 Jun 2020 22:33:15: 7000000 INFO @ Sun, 21 Jun 2020 22:33:18: 2000000 INFO @ Sun, 21 Jun 2020 22:33:21: 8000000 INFO @ Sun, 21 Jun 2020 22:33:24: 3000000 INFO @ Sun, 21 Jun 2020 22:33:28: 9000000 INFO @ Sun, 21 Jun 2020 22:33:31: 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 22:33:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.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 22:33:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:33:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:33:34: 10000000 INFO @ Sun, 21 Jun 2020 22:33:37: 5000000 INFO @ Sun, 21 Jun 2020 22:33:41: 11000000 INFO @ Sun, 21 Jun 2020 22:33:41: 1000000 INFO @ Sun, 21 Jun 2020 22:33:44: 6000000 INFO @ Sun, 21 Jun 2020 22:33:48: 12000000 INFO @ Sun, 21 Jun 2020 22:33:48: 2000000 INFO @ Sun, 21 Jun 2020 22:33:51: 7000000 INFO @ Sun, 21 Jun 2020 22:33:51: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 22:33:51: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 22:33:51: #1 total tags in treatment: 12418521 INFO @ Sun, 21 Jun 2020 22:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:33:51: #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 22:33:52: #1 tags after filtering in treatment: 12418453 INFO @ Sun, 21 Jun 2020 22:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:33:52: #1 finished! INFO @ Sun, 21 Jun 2020 22:33:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:33:53: #2 number of paired peaks: 545 WARNING @ Sun, 21 Jun 2020 22:33:53: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Sun, 21 Jun 2020 22:33:53: start model_add_line... INFO @ Sun, 21 Jun 2020 22:33:53: start X-correlation... INFO @ Sun, 21 Jun 2020 22:33:53: end of X-cor INFO @ Sun, 21 Jun 2020 22:33:53: #2 finished! INFO @ Sun, 21 Jun 2020 22:33:53: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:33:53: #2 alternative fragment length(s) may be 2,27 bps INFO @ Sun, 21 Jun 2020 22:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.05_model.r WARNING @ Sun, 21 Jun 2020 22:33:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:33:53: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Sun, 21 Jun 2020 22:33:53: #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 22:33:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:33:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:33:55: 3000000 INFO @ Sun, 21 Jun 2020 22:33:58: 8000000 INFO @ Sun, 21 Jun 2020 22:34:02: 4000000 INFO @ Sun, 21 Jun 2020 22:34:04: 9000000 INFO @ Sun, 21 Jun 2020 22:34:09: 5000000 INFO @ Sun, 21 Jun 2020 22:34:11: 10000000 INFO @ Sun, 21 Jun 2020 22:34:15: 6000000 INFO @ Sun, 21 Jun 2020 22:34:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:34:18: 11000000 INFO @ Sun, 21 Jun 2020 22:34:22: 7000000 INFO @ Sun, 21 Jun 2020 22:34:25: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:34:28: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 22:34:28: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 22:34:28: #1 total tags in treatment: 12418521 INFO @ Sun, 21 Jun 2020 22:34:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:28: #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 22:34:28: #1 tags after filtering in treatment: 12418453 INFO @ Sun, 21 Jun 2020 22:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:29: 8000000 INFO @ Sun, 21 Jun 2020 22:34:29: #2 number of paired peaks: 545 WARNING @ Sun, 21 Jun 2020 22:34:29: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Sun, 21 Jun 2020 22:34:29: start model_add_line... INFO @ Sun, 21 Jun 2020 22:34:29: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:29: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:29: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:29: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:34:29: #2 alternative fragment length(s) may be 2,27 bps INFO @ Sun, 21 Jun 2020 22:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.10_model.r WARNING @ Sun, 21 Jun 2020 22:34:29: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:34:29: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Sun, 21 Jun 2020 22:34:29: #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 22:34:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.05_summits.bed INFO @ Sun, 21 Jun 2020 22:34:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:34:35: 9000000 INFO @ Sun, 21 Jun 2020 22:34:42: 10000000 INFO @ Sun, 21 Jun 2020 22:34:48: 11000000 INFO @ Sun, 21 Jun 2020 22:34:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:34:55: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:34:57: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 22:34:57: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 22:34:57: #1 total tags in treatment: 12418521 INFO @ Sun, 21 Jun 2020 22:34:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:57: #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 22:34:58: #1 tags after filtering in treatment: 12418453 INFO @ Sun, 21 Jun 2020 22:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:58: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:59: #2 number of paired peaks: 545 WARNING @ Sun, 21 Jun 2020 22:34:59: Fewer paired peaks (545) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 545 pairs to build model! INFO @ Sun, 21 Jun 2020 22:34:59: start model_add_line... INFO @ Sun, 21 Jun 2020 22:34:59: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:59: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:59: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:59: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 22:34:59: #2 alternative fragment length(s) may be 2,27 bps INFO @ Sun, 21 Jun 2020 22:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.20_model.r WARNING @ Sun, 21 Jun 2020 22:34:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:34:59: #2 You may need to consider one of the other alternative d(s): 2,27 WARNING @ Sun, 21 Jun 2020 22:34:59: #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 22:34:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:35:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.10_summits.bed INFO @ Sun, 21 Jun 2020 22:35:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:35:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7299239/SRX7299239.20_summits.bed INFO @ Sun, 21 Jun 2020 22:35:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling