Job ID = 6458081 SRX = SRX495208 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:06:51 prefetch.2.10.7: 1) Downloading 'SRR1198713'... 2020-06-21T12:06:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:08:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:08:52 prefetch.2.10.7: 1) 'SRR1198713' was downloaded successfully Read 22251934 spots for SRR1198713/SRR1198713.sra Written 22251934 spots for SRR1198713/SRR1198713.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: 00:05:46 22251934 reads; of these: 22251934 (100.00%) were unpaired; of these: 973197 (4.37%) aligned 0 times 15054277 (67.65%) aligned exactly 1 time 6224460 (27.97%) aligned >1 times 95.63% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5990334 / 21278737 = 0.2815 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 21:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.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 21:20:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:20:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:20:50: 1000000 INFO @ Sun, 21 Jun 2020 21:20:56: 2000000 INFO @ Sun, 21 Jun 2020 21:21:02: 3000000 INFO @ Sun, 21 Jun 2020 21:21:09: 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 21:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.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 21:21:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:16: 5000000 INFO @ Sun, 21 Jun 2020 21:21:19: 1000000 INFO @ Sun, 21 Jun 2020 21:21:22: 6000000 INFO @ Sun, 21 Jun 2020 21:21:25: 2000000 INFO @ Sun, 21 Jun 2020 21:21:29: 7000000 INFO @ Sun, 21 Jun 2020 21:21:31: 3000000 INFO @ Sun, 21 Jun 2020 21:21:35: 8000000 INFO @ Sun, 21 Jun 2020 21:21:37: 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 21:21:42: 9000000 INFO @ Sun, 21 Jun 2020 21:21:43: 5000000 INFO @ Sun, 21 Jun 2020 21:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.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 21:21:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:21:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:21:49: 10000000 INFO @ Sun, 21 Jun 2020 21:21:49: 6000000 INFO @ Sun, 21 Jun 2020 21:21:50: 1000000 INFO @ Sun, 21 Jun 2020 21:21:55: 7000000 INFO @ Sun, 21 Jun 2020 21:21:55: 11000000 INFO @ Sun, 21 Jun 2020 21:21:57: 2000000 INFO @ Sun, 21 Jun 2020 21:22:01: 8000000 INFO @ Sun, 21 Jun 2020 21:22:02: 12000000 INFO @ Sun, 21 Jun 2020 21:22:04: 3000000 INFO @ Sun, 21 Jun 2020 21:22:07: 9000000 INFO @ Sun, 21 Jun 2020 21:22:09: 13000000 INFO @ Sun, 21 Jun 2020 21:22:10: 4000000 INFO @ Sun, 21 Jun 2020 21:22:13: 10000000 INFO @ Sun, 21 Jun 2020 21:22:16: 14000000 INFO @ Sun, 21 Jun 2020 21:22:17: 5000000 INFO @ Sun, 21 Jun 2020 21:22:19: 11000000 INFO @ Sun, 21 Jun 2020 21:22:22: 15000000 INFO @ Sun, 21 Jun 2020 21:22:24: 6000000 INFO @ Sun, 21 Jun 2020 21:22:24: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:22:24: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:22:24: #1 total tags in treatment: 15288403 INFO @ Sun, 21 Jun 2020 21:22:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:24: #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 21:22:25: 12000000 INFO @ Sun, 21 Jun 2020 21:22:25: #1 tags after filtering in treatment: 15288403 INFO @ Sun, 21 Jun 2020 21:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:25: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:26: #2 number of paired peaks: 101 WARNING @ Sun, 21 Jun 2020 21:22:26: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 21 Jun 2020 21:22:26: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:26: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:26: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:26: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:26: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 21:22:26: #2 alternative fragment length(s) may be 4,10,41,63,513 bps INFO @ Sun, 21 Jun 2020 21:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.05_model.r WARNING @ Sun, 21 Jun 2020 21:22:26: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:26: #2 You may need to consider one of the other alternative d(s): 4,10,41,63,513 WARNING @ Sun, 21 Jun 2020 21:22:26: #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 21:22:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:30: 7000000 INFO @ Sun, 21 Jun 2020 21:22:31: 13000000 INFO @ Sun, 21 Jun 2020 21:22:37: 14000000 INFO @ Sun, 21 Jun 2020 21:22:37: 8000000 INFO @ Sun, 21 Jun 2020 21:22:43: 15000000 INFO @ Sun, 21 Jun 2020 21:22:44: 9000000 INFO @ Sun, 21 Jun 2020 21:22:45: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:22:45: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:22:45: #1 total tags in treatment: 15288403 INFO @ Sun, 21 Jun 2020 21:22:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:22:45: #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 21:22:45: #1 tags after filtering in treatment: 15288403 INFO @ Sun, 21 Jun 2020 21:22:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:22:45: #1 finished! INFO @ Sun, 21 Jun 2020 21:22:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:22:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:22:46: #2 number of paired peaks: 101 WARNING @ Sun, 21 Jun 2020 21:22:46: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 21 Jun 2020 21:22:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:22:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:22:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:22:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:22:46: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 21:22:46: #2 alternative fragment length(s) may be 4,10,41,63,513 bps INFO @ Sun, 21 Jun 2020 21:22:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.10_model.r WARNING @ Sun, 21 Jun 2020 21:22:46: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:22:46: #2 You may need to consider one of the other alternative d(s): 4,10,41,63,513 WARNING @ Sun, 21 Jun 2020 21:22:46: #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 21:22:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:22:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:22:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:22:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:56: 11000000 INFO @ Sun, 21 Jun 2020 21:23:02: 12000000 INFO @ Sun, 21 Jun 2020 21:23:09: 13000000 INFO @ Sun, 21 Jun 2020 21:23:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.05_summits.bed INFO @ Sun, 21 Jun 2020 21:23:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:15: 14000000 INFO @ Sun, 21 Jun 2020 21:23:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:23:21: 15000000 INFO @ Sun, 21 Jun 2020 21:23:23: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:23:23: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:23:23: #1 total tags in treatment: 15288403 INFO @ Sun, 21 Jun 2020 21:23:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:23:23: #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 21:23:23: #1 tags after filtering in treatment: 15288403 INFO @ Sun, 21 Jun 2020 21:23:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:23:23: #1 finished! INFO @ Sun, 21 Jun 2020 21:23:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:23:24: #2 number of paired peaks: 101 WARNING @ Sun, 21 Jun 2020 21:23:24: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Sun, 21 Jun 2020 21:23:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:23:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:23:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:23:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:23:24: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 21:23:24: #2 alternative fragment length(s) may be 4,10,41,63,513 bps INFO @ Sun, 21 Jun 2020 21:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.20_model.r WARNING @ Sun, 21 Jun 2020 21:23:24: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:23:24: #2 You may need to consider one of the other alternative d(s): 4,10,41,63,513 WARNING @ Sun, 21 Jun 2020 21:23:24: #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 21:23:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:23:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:23:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:23:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:23:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.10_summits.bed INFO @ Sun, 21 Jun 2020 21:23:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:23:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495208/SRX495208.20_summits.bed INFO @ Sun, 21 Jun 2020 21:24:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling