Job ID = 6453721 SRX = SRX1433364 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:35:09 prefetch.2.10.7: 1) Downloading 'SRR2919829'... 2020-06-21T08:35:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:37:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:37:39 prefetch.2.10.7: 'SRR2919829' is valid 2020-06-21T08:37:39 prefetch.2.10.7: 1) 'SRR2919829' was downloaded successfully Read 20538046 spots for SRR2919829/SRR2919829.sra Written 20538046 spots for SRR2919829/SRR2919829.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: 00:06:06 20538046 reads; of these: 20538046 (100.00%) were unpaired; of these: 554507 (2.70%) aligned 0 times 15089864 (73.47%) aligned exactly 1 time 4893675 (23.83%) aligned >1 times 97.30% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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 12 files... [bam_rmdupse_core] 3292995 / 19983539 = 0.1648 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 17:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.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 17:49:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:01: 1000000 INFO @ Sun, 21 Jun 2020 17:50:06: 2000000 INFO @ Sun, 21 Jun 2020 17:50:11: 3000000 INFO @ Sun, 21 Jun 2020 17:50:16: 4000000 INFO @ Sun, 21 Jun 2020 17:50:21: 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 17:50:26: 6000000 INFO @ Sun, 21 Jun 2020 17:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.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 17:50:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:31: 7000000 INFO @ Sun, 21 Jun 2020 17:50:32: 1000000 INFO @ Sun, 21 Jun 2020 17:50:36: 8000000 INFO @ Sun, 21 Jun 2020 17:50:37: 2000000 INFO @ Sun, 21 Jun 2020 17:50:42: 9000000 INFO @ Sun, 21 Jun 2020 17:50:43: 3000000 INFO @ Sun, 21 Jun 2020 17:50:47: 10000000 INFO @ Sun, 21 Jun 2020 17:50:48: 4000000 INFO @ Sun, 21 Jun 2020 17:50:52: 11000000 INFO @ Sun, 21 Jun 2020 17:50:53: 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 17:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.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 17:50:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:57: 12000000 INFO @ Sun, 21 Jun 2020 17:50:58: 6000000 INFO @ Sun, 21 Jun 2020 17:51:02: 1000000 INFO @ Sun, 21 Jun 2020 17:51:02: 13000000 INFO @ Sun, 21 Jun 2020 17:51:03: 7000000 INFO @ Sun, 21 Jun 2020 17:51:07: 2000000 INFO @ Sun, 21 Jun 2020 17:51:08: 14000000 INFO @ Sun, 21 Jun 2020 17:51:09: 8000000 INFO @ Sun, 21 Jun 2020 17:51:13: 3000000 INFO @ Sun, 21 Jun 2020 17:51:14: 15000000 INFO @ Sun, 21 Jun 2020 17:51:14: 9000000 INFO @ Sun, 21 Jun 2020 17:51:19: 4000000 INFO @ Sun, 21 Jun 2020 17:51:19: 16000000 INFO @ Sun, 21 Jun 2020 17:51:19: 10000000 INFO @ Sun, 21 Jun 2020 17:51:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:51:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:51:23: #1 total tags in treatment: 16690544 INFO @ Sun, 21 Jun 2020 17:51:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:23: #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 17:51:24: 5000000 INFO @ Sun, 21 Jun 2020 17:51:24: #1 tags after filtering in treatment: 16690481 INFO @ Sun, 21 Jun 2020 17:51:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:24: 11000000 INFO @ Sun, 21 Jun 2020 17:51:25: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 17:51:25: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 17:51:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:25: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:51:25: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 17:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.05_model.r WARNING @ Sun, 21 Jun 2020 17:51:25: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:25: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 17:51:25: #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 17:51:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:51:29: 6000000 INFO @ Sun, 21 Jun 2020 17:51:29: 12000000 INFO @ Sun, 21 Jun 2020 17:51:34: 13000000 INFO @ Sun, 21 Jun 2020 17:51:34: 7000000 INFO @ Sun, 21 Jun 2020 17:51:39: 8000000 INFO @ Sun, 21 Jun 2020 17:51:40: 14000000 INFO @ Sun, 21 Jun 2020 17:51:44: 9000000 INFO @ Sun, 21 Jun 2020 17:51:45: 15000000 INFO @ Sun, 21 Jun 2020 17:51:49: 10000000 INFO @ Sun, 21 Jun 2020 17:51:50: 16000000 INFO @ Sun, 21 Jun 2020 17:51:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:51:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:51:53: #1 total tags in treatment: 16690544 INFO @ Sun, 21 Jun 2020 17:51:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:53: #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 17:51:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:54: #1 tags after filtering in treatment: 16690481 INFO @ Sun, 21 Jun 2020 17:51:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:54: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:54: 11000000 INFO @ Sun, 21 Jun 2020 17:51:55: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 17:51:55: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 17:51:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:55: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:51:55: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 17:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.10_model.r WARNING @ Sun, 21 Jun 2020 17:51:55: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:51:55: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 17:51:55: #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 17:51:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:51:59: 12000000 INFO @ Sun, 21 Jun 2020 17:52:04: 13000000 INFO @ Sun, 21 Jun 2020 17:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:08: Done! pass1 - making usageList (402 chroms): 2 millis pass2 - checking and writing primary data (1404 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:10: 14000000 INFO @ Sun, 21 Jun 2020 17:52:15: 15000000 INFO @ Sun, 21 Jun 2020 17:52:20: 16000000 INFO @ Sun, 21 Jun 2020 17:52:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:52:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:52:24: #1 total tags in treatment: 16690544 INFO @ Sun, 21 Jun 2020 17:52:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:24: #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 17:52:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:25: #1 tags after filtering in treatment: 16690481 INFO @ Sun, 21 Jun 2020 17:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:25: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:26: #2 number of paired peaks: 276 WARNING @ Sun, 21 Jun 2020 17:52:26: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Sun, 21 Jun 2020 17:52:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:26: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 17:52:26: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sun, 21 Jun 2020 17:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.20_model.r WARNING @ Sun, 21 Jun 2020 17:52:26: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:26: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sun, 21 Jun 2020 17:52:26: #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 17:52:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.10_summits.bed INFO @ Sun, 21 Jun 2020 17:52:39: Done! pass1 - making usageList (204 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433364/SRX1433364.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:10: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。