Job ID = 6455008 SRX = SRX2618553 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:40 prefetch.2.10.7: 1) Downloading 'SRR5319107'... 2020-06-21T09:40:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:43:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:43:18 prefetch.2.10.7: 1) 'SRR5319107' was downloaded successfully 2020-06-21T09:43:18 prefetch.2.10.7: 'SRR5319107' has 0 unresolved dependencies Read 28023752 spots for SRR5319107/SRR5319107.sra Written 28023752 spots for SRR5319107/SRR5319107.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: 00:07:51 28023752 reads; of these: 28023752 (100.00%) were unpaired; of these: 1005418 (3.59%) aligned 0 times 19613522 (69.99%) aligned exactly 1 time 7404812 (26.42%) aligned >1 times 96.41% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 4230812 / 27018334 = 0.1566 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 18:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.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 18:58:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:32: 1000000 INFO @ Sun, 21 Jun 2020 18:58:38: 2000000 INFO @ Sun, 21 Jun 2020 18:58:43: 3000000 INFO @ Sun, 21 Jun 2020 18:58:49: 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 18:58:54: 5000000 INFO @ Sun, 21 Jun 2020 18:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.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 18:58:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:00: 6000000 INFO @ Sun, 21 Jun 2020 18:59:02: 1000000 INFO @ Sun, 21 Jun 2020 18:59:06: 7000000 INFO @ Sun, 21 Jun 2020 18:59:08: 2000000 INFO @ Sun, 21 Jun 2020 18:59:12: 8000000 INFO @ Sun, 21 Jun 2020 18:59:14: 3000000 INFO @ Sun, 21 Jun 2020 18:59:17: 9000000 INFO @ Sun, 21 Jun 2020 18:59:19: 4000000 INFO @ Sun, 21 Jun 2020 18:59:23: 10000000 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 18:59:25: 5000000 INFO @ Sun, 21 Jun 2020 18:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.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 18:59:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:59:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:59:29: 11000000 INFO @ Sun, 21 Jun 2020 18:59:31: 6000000 INFO @ Sun, 21 Jun 2020 18:59:31: 1000000 INFO @ Sun, 21 Jun 2020 18:59:34: 12000000 INFO @ Sun, 21 Jun 2020 18:59:36: 2000000 INFO @ Sun, 21 Jun 2020 18:59:37: 7000000 INFO @ Sun, 21 Jun 2020 18:59:40: 13000000 INFO @ Sun, 21 Jun 2020 18:59:42: 3000000 INFO @ Sun, 21 Jun 2020 18:59:43: 8000000 INFO @ Sun, 21 Jun 2020 18:59:46: 14000000 INFO @ Sun, 21 Jun 2020 18:59:47: 4000000 INFO @ Sun, 21 Jun 2020 18:59:48: 9000000 INFO @ Sun, 21 Jun 2020 18:59:52: 15000000 INFO @ Sun, 21 Jun 2020 18:59:52: 5000000 INFO @ Sun, 21 Jun 2020 18:59:54: 10000000 INFO @ Sun, 21 Jun 2020 18:59:57: 6000000 INFO @ Sun, 21 Jun 2020 18:59:57: 16000000 INFO @ Sun, 21 Jun 2020 19:00:00: 11000000 INFO @ Sun, 21 Jun 2020 19:00:02: 7000000 INFO @ Sun, 21 Jun 2020 19:00:03: 17000000 INFO @ Sun, 21 Jun 2020 19:00:06: 12000000 INFO @ Sun, 21 Jun 2020 19:00:07: 8000000 INFO @ Sun, 21 Jun 2020 19:00:09: 18000000 INFO @ Sun, 21 Jun 2020 19:00:11: 13000000 INFO @ Sun, 21 Jun 2020 19:00:12: 9000000 INFO @ Sun, 21 Jun 2020 19:00:15: 19000000 INFO @ Sun, 21 Jun 2020 19:00:17: 10000000 INFO @ Sun, 21 Jun 2020 19:00:17: 14000000 INFO @ Sun, 21 Jun 2020 19:00:20: 20000000 INFO @ Sun, 21 Jun 2020 19:00:22: 11000000 INFO @ Sun, 21 Jun 2020 19:00:23: 15000000 INFO @ Sun, 21 Jun 2020 19:00:26: 21000000 INFO @ Sun, 21 Jun 2020 19:00:27: 12000000 INFO @ Sun, 21 Jun 2020 19:00:28: 16000000 INFO @ Sun, 21 Jun 2020 19:00:32: 22000000 INFO @ Sun, 21 Jun 2020 19:00:32: 13000000 INFO @ Sun, 21 Jun 2020 19:00:34: 17000000 INFO @ Sun, 21 Jun 2020 19:00:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:00:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:00:36: #1 total tags in treatment: 22787522 INFO @ Sun, 21 Jun 2020 19:00:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:00:36: #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 19:00:37: #1 tags after filtering in treatment: 22787521 INFO @ Sun, 21 Jun 2020 19:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:00:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:00:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:00:37: 14000000 INFO @ Sun, 21 Jun 2020 19:00:38: #2 number of paired peaks: 613 WARNING @ Sun, 21 Jun 2020 19:00:38: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Sun, 21 Jun 2020 19:00:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:00:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:00:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:00:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:00:39: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:00:39: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 19:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.05_model.r WARNING @ Sun, 21 Jun 2020 19:00:39: #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 19:00:39: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 19:00:39: #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 19:00:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:00:40: 18000000 INFO @ Sun, 21 Jun 2020 19:00:42: 15000000 INFO @ Sun, 21 Jun 2020 19:00:45: 19000000 INFO @ Sun, 21 Jun 2020 19:00:48: 16000000 INFO @ Sun, 21 Jun 2020 19:00:51: 20000000 INFO @ Sun, 21 Jun 2020 19:00:53: 17000000 INFO @ Sun, 21 Jun 2020 19:00:56: 21000000 INFO @ Sun, 21 Jun 2020 19:00:58: 18000000 INFO @ Sun, 21 Jun 2020 19:01:02: 22000000 INFO @ Sun, 21 Jun 2020 19:01:03: 19000000 INFO @ Sun, 21 Jun 2020 19:01:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:07: #1 total tags in treatment: 22787522 INFO @ Sun, 21 Jun 2020 19:01:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:07: #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 19:01:08: #1 tags after filtering in treatment: 22787521 INFO @ Sun, 21 Jun 2020 19:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:09: 20000000 INFO @ Sun, 21 Jun 2020 19:01:09: #2 number of paired peaks: 613 WARNING @ Sun, 21 Jun 2020 19:01:09: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:09: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:09: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:01:09: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 19:01:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.10_model.r WARNING @ Sun, 21 Jun 2020 19:01:09: #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 19:01:09: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 19:01:09: #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 19:01:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:14: 21000000 INFO @ Sun, 21 Jun 2020 19:01:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:01:20: 22000000 INFO @ Sun, 21 Jun 2020 19:01:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:01:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:01:24: #1 total tags in treatment: 22787522 INFO @ Sun, 21 Jun 2020 19:01:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:01:24: #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 19:01:25: #1 tags after filtering in treatment: 22787521 INFO @ Sun, 21 Jun 2020 19:01:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:01:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:01:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:01:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:01:26: #2 number of paired peaks: 613 WARNING @ Sun, 21 Jun 2020 19:01:26: Fewer paired peaks (613) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 613 pairs to build model! INFO @ Sun, 21 Jun 2020 19:01:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:01:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:01:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:01:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:01:26: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:01:26: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 19:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.20_model.r WARNING @ Sun, 21 Jun 2020 19:01:26: #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 19:01:26: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 19:01:26: #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 19:01:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.05_summits.bed INFO @ Sun, 21 Jun 2020 19:01:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:01:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.10_summits.bed INFO @ Sun, 21 Jun 2020 19:02:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:02:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:02:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:02:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618553/SRX2618553.20_summits.bed INFO @ Sun, 21 Jun 2020 19:02:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling