Job ID = 6454968 SRX = SRX2618511 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:35:40 prefetch.2.10.7: 1) Downloading 'SRR5319065'... 2020-06-21T09:35:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:41:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:41:07 prefetch.2.10.7: 1) 'SRR5319065' was downloaded successfully 2020-06-21T09:41:07 prefetch.2.10.7: 'SRR5319065' has 0 unresolved dependencies Read 45397592 spots for SRR5319065/SRR5319065.sra Written 45397592 spots for SRR5319065/SRR5319065.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: 00:09:09 45397592 reads; of these: 45397592 (100.00%) were unpaired; of these: 14869821 (32.75%) aligned 0 times 23756667 (52.33%) aligned exactly 1 time 6771104 (14.92%) aligned >1 times 67.25% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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 16 files... [bam_rmdupse_core] 4845452 / 30527771 = 0.1587 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 19:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.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 19:01:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:16: 1000000 INFO @ Sun, 21 Jun 2020 19:01:23: 2000000 INFO @ Sun, 21 Jun 2020 19:01:30: 3000000 INFO @ Sun, 21 Jun 2020 19:01:36: 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 19:01:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.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 19:01:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:01:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:01:43: 5000000 INFO @ Sun, 21 Jun 2020 19:01:47: 1000000 INFO @ Sun, 21 Jun 2020 19:01:49: 6000000 INFO @ Sun, 21 Jun 2020 19:01:53: 2000000 INFO @ Sun, 21 Jun 2020 19:01:56: 7000000 INFO @ Sun, 21 Jun 2020 19:02:00: 3000000 INFO @ Sun, 21 Jun 2020 19:02:02: 8000000 INFO @ Sun, 21 Jun 2020 19:02:07: 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 19:02:09: 9000000 INFO @ Sun, 21 Jun 2020 19:02:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.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 19:02:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:13: 5000000 INFO @ Sun, 21 Jun 2020 19:02:15: 10000000 INFO @ Sun, 21 Jun 2020 19:02:17: 1000000 INFO @ Sun, 21 Jun 2020 19:02:20: 6000000 INFO @ Sun, 21 Jun 2020 19:02:22: 11000000 INFO @ Sun, 21 Jun 2020 19:02:24: 2000000 INFO @ Sun, 21 Jun 2020 19:02:27: 7000000 INFO @ Sun, 21 Jun 2020 19:02:29: 12000000 INFO @ Sun, 21 Jun 2020 19:02:32: 3000000 INFO @ Sun, 21 Jun 2020 19:02:33: 8000000 INFO @ Sun, 21 Jun 2020 19:02:36: 13000000 INFO @ Sun, 21 Jun 2020 19:02:39: 4000000 INFO @ Sun, 21 Jun 2020 19:02:40: 9000000 INFO @ Sun, 21 Jun 2020 19:02:43: 14000000 INFO @ Sun, 21 Jun 2020 19:02:45: 5000000 INFO @ Sun, 21 Jun 2020 19:02:47: 10000000 INFO @ Sun, 21 Jun 2020 19:02:49: 15000000 INFO @ Sun, 21 Jun 2020 19:02:52: 6000000 INFO @ Sun, 21 Jun 2020 19:02:53: 11000000 INFO @ Sun, 21 Jun 2020 19:02:56: 16000000 INFO @ Sun, 21 Jun 2020 19:02:59: 7000000 INFO @ Sun, 21 Jun 2020 19:03:00: 12000000 INFO @ Sun, 21 Jun 2020 19:03:03: 17000000 INFO @ Sun, 21 Jun 2020 19:03:05: 8000000 INFO @ Sun, 21 Jun 2020 19:03:06: 13000000 INFO @ Sun, 21 Jun 2020 19:03:10: 18000000 INFO @ Sun, 21 Jun 2020 19:03:12: 9000000 INFO @ Sun, 21 Jun 2020 19:03:13: 14000000 INFO @ Sun, 21 Jun 2020 19:03:17: 19000000 INFO @ Sun, 21 Jun 2020 19:03:18: 10000000 INFO @ Sun, 21 Jun 2020 19:03:19: 15000000 INFO @ Sun, 21 Jun 2020 19:03:24: 20000000 INFO @ Sun, 21 Jun 2020 19:03:25: 11000000 INFO @ Sun, 21 Jun 2020 19:03:26: 16000000 INFO @ Sun, 21 Jun 2020 19:03:31: 12000000 INFO @ Sun, 21 Jun 2020 19:03:31: 21000000 INFO @ Sun, 21 Jun 2020 19:03:32: 17000000 INFO @ Sun, 21 Jun 2020 19:03:37: 13000000 INFO @ Sun, 21 Jun 2020 19:03:38: 22000000 INFO @ Sun, 21 Jun 2020 19:03:39: 18000000 INFO @ Sun, 21 Jun 2020 19:03:44: 14000000 INFO @ Sun, 21 Jun 2020 19:03:44: 23000000 INFO @ Sun, 21 Jun 2020 19:03:45: 19000000 INFO @ Sun, 21 Jun 2020 19:03:50: 15000000 INFO @ Sun, 21 Jun 2020 19:03:51: 24000000 INFO @ Sun, 21 Jun 2020 19:03:52: 20000000 INFO @ Sun, 21 Jun 2020 19:03:56: 16000000 INFO @ Sun, 21 Jun 2020 19:03:57: 25000000 INFO @ Sun, 21 Jun 2020 19:03:58: 21000000 INFO @ Sun, 21 Jun 2020 19:04:02: 17000000 INFO @ Sun, 21 Jun 2020 19:04:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:02: #1 total tags in treatment: 25682319 INFO @ Sun, 21 Jun 2020 19:04:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:02: #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 19:04:03: #1 tags after filtering in treatment: 25682318 INFO @ Sun, 21 Jun 2020 19:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:04: 22000000 INFO @ Sun, 21 Jun 2020 19:04:05: #2 number of paired peaks: 486 WARNING @ Sun, 21 Jun 2020 19:04:05: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:05: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:04:05: #2 alternative fragment length(s) may be 2,34 bps INFO @ Sun, 21 Jun 2020 19:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.05_model.r WARNING @ Sun, 21 Jun 2020 19:04:05: #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 19:04:05: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Sun, 21 Jun 2020 19:04:05: #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 19:04:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:08: 18000000 INFO @ Sun, 21 Jun 2020 19:04:10: 23000000 INFO @ Sun, 21 Jun 2020 19:04:13: 19000000 INFO @ Sun, 21 Jun 2020 19:04:15: 24000000 INFO @ Sun, 21 Jun 2020 19:04:19: 20000000 INFO @ Sun, 21 Jun 2020 19:04:21: 25000000 INFO @ Sun, 21 Jun 2020 19:04:25: 21000000 INFO @ Sun, 21 Jun 2020 19:04:25: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:25: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:25: #1 total tags in treatment: 25682319 INFO @ Sun, 21 Jun 2020 19:04:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:25: #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 19:04:26: #1 tags after filtering in treatment: 25682318 INFO @ Sun, 21 Jun 2020 19:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:28: #2 number of paired peaks: 486 WARNING @ Sun, 21 Jun 2020 19:04:28: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:28: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:04:28: #2 alternative fragment length(s) may be 2,34 bps INFO @ Sun, 21 Jun 2020 19:04:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:28: #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 19:04:28: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Sun, 21 Jun 2020 19:04:28: #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 19:04:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:30: 22000000 INFO @ Sun, 21 Jun 2020 19:04:35: 23000000 INFO @ Sun, 21 Jun 2020 19:04:41: 24000000 INFO @ Sun, 21 Jun 2020 19:04:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:46: 25000000 INFO @ Sun, 21 Jun 2020 19:04:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:04:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:04:50: #1 total tags in treatment: 25682319 INFO @ Sun, 21 Jun 2020 19:04:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:50: #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 19:04:51: #1 tags after filtering in treatment: 25682318 INFO @ Sun, 21 Jun 2020 19:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:53: #2 number of paired peaks: 486 WARNING @ Sun, 21 Jun 2020 19:04:53: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Sun, 21 Jun 2020 19:04:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:53: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:04:53: #2 alternative fragment length(s) may be 2,34 bps INFO @ Sun, 21 Jun 2020 19:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.20_model.r WARNING @ Sun, 21 Jun 2020 19:04:53: #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 19:04:53: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Sun, 21 Jun 2020 19:04:53: #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 19:04:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.05_summits.bed INFO @ Sun, 21 Jun 2020 19:05:01: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:24: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618511/SRX2618511.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling