Job ID = 5720405 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,972,440 reads read : 29,972,440 reads written : 29,972,440 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289671.sra.cache’: No such file or directory 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: 00:10:17 29972440 reads; of these: 29972440 (100.00%) were unpaired; of these: 1917418 (6.40%) aligned 0 times 20681977 (69.00%) aligned exactly 1 time 7373045 (24.60%) aligned >1 times 93.60% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6614156 / 28055022 = 0.2358 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 @ Thu, 16 Apr 2020 00:38:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.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 @ Thu, 16 Apr 2020 00:38:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:56: 1000000 INFO @ Thu, 16 Apr 2020 00:39:02: 2000000 INFO @ Thu, 16 Apr 2020 00:39:07: 3000000 INFO @ Thu, 16 Apr 2020 00:39:12: 4000000 INFO @ Thu, 16 Apr 2020 00:39:17: 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 @ Thu, 16 Apr 2020 00:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.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 @ Thu, 16 Apr 2020 00:39:21: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:21: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:23: 6000000 INFO @ Thu, 16 Apr 2020 00:39:27: 1000000 INFO @ Thu, 16 Apr 2020 00:39:29: 7000000 INFO @ Thu, 16 Apr 2020 00:39:33: 2000000 INFO @ Thu, 16 Apr 2020 00:39:35: 8000000 INFO @ Thu, 16 Apr 2020 00:39:38: 3000000 INFO @ Thu, 16 Apr 2020 00:39:40: 9000000 INFO @ Thu, 16 Apr 2020 00:39:44: 4000000 INFO @ Thu, 16 Apr 2020 00:39:46: 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 @ Thu, 16 Apr 2020 00:39:50: 5000000 INFO @ Thu, 16 Apr 2020 00:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.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 @ Thu, 16 Apr 2020 00:39:51: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:51: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:52: 11000000 INFO @ Thu, 16 Apr 2020 00:39:56: 6000000 INFO @ Thu, 16 Apr 2020 00:39:57: 1000000 INFO @ Thu, 16 Apr 2020 00:39:58: 12000000 INFO @ Thu, 16 Apr 2020 00:40:02: 7000000 INFO @ Thu, 16 Apr 2020 00:40:03: 2000000 INFO @ Thu, 16 Apr 2020 00:40:04: 13000000 INFO @ Thu, 16 Apr 2020 00:40:08: 8000000 INFO @ Thu, 16 Apr 2020 00:40:09: 3000000 INFO @ Thu, 16 Apr 2020 00:40:10: 14000000 INFO @ Thu, 16 Apr 2020 00:40:14: 9000000 INFO @ Thu, 16 Apr 2020 00:40:15: 4000000 INFO @ Thu, 16 Apr 2020 00:40:16: 15000000 INFO @ Thu, 16 Apr 2020 00:40:20: 10000000 INFO @ Thu, 16 Apr 2020 00:40:21: 5000000 INFO @ Thu, 16 Apr 2020 00:40:22: 16000000 INFO @ Thu, 16 Apr 2020 00:40:26: 11000000 INFO @ Thu, 16 Apr 2020 00:40:27: 6000000 INFO @ Thu, 16 Apr 2020 00:40:28: 17000000 INFO @ Thu, 16 Apr 2020 00:40:32: 12000000 INFO @ Thu, 16 Apr 2020 00:40:33: 7000000 INFO @ Thu, 16 Apr 2020 00:40:34: 18000000 INFO @ Thu, 16 Apr 2020 00:40:38: 13000000 INFO @ Thu, 16 Apr 2020 00:40:39: 8000000 INFO @ Thu, 16 Apr 2020 00:40:40: 19000000 INFO @ Thu, 16 Apr 2020 00:40:44: 14000000 INFO @ Thu, 16 Apr 2020 00:40:45: 9000000 INFO @ Thu, 16 Apr 2020 00:40:46: 20000000 INFO @ Thu, 16 Apr 2020 00:40:50: 15000000 INFO @ Thu, 16 Apr 2020 00:40:51: 10000000 INFO @ Thu, 16 Apr 2020 00:40:52: 21000000 INFO @ Thu, 16 Apr 2020 00:40:55: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:40:55: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:40:55: #1 total tags in treatment: 21440866 INFO @ Thu, 16 Apr 2020 00:40:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:40:55: #1 tags after filtering in treatment: 21440866 INFO @ Thu, 16 Apr 2020 00:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:55: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:55: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:56: 16000000 INFO @ Thu, 16 Apr 2020 00:40:57: #2 number of paired peaks: 128 WARNING @ Thu, 16 Apr 2020 00:40:57: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:57: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:57: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:57: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:57: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:57: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:40:57: #2 alternative fragment length(s) may be 3,55,346 bps INFO @ Thu, 16 Apr 2020 00:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.05_model.r WARNING @ Thu, 16 Apr 2020 00:40:57: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:40:57: #2 You may need to consider one of the other alternative d(s): 3,55,346 WARNING @ Thu, 16 Apr 2020 00:40:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:40:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:40:58: 11000000 INFO @ Thu, 16 Apr 2020 00:41:03: 17000000 INFO @ Thu, 16 Apr 2020 00:41:04: 12000000 INFO @ Thu, 16 Apr 2020 00:41:09: 18000000 INFO @ Thu, 16 Apr 2020 00:41:10: 13000000 INFO @ Thu, 16 Apr 2020 00:41:15: 19000000 INFO @ Thu, 16 Apr 2020 00:41:16: 14000000 INFO @ Thu, 16 Apr 2020 00:41:22: 20000000 INFO @ Thu, 16 Apr 2020 00:41:22: 15000000 INFO @ Thu, 16 Apr 2020 00:41:28: 21000000 INFO @ Thu, 16 Apr 2020 00:41:29: 16000000 INFO @ Thu, 16 Apr 2020 00:41:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:41:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:41:30: #1 total tags in treatment: 21440866 INFO @ Thu, 16 Apr 2020 00:41:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:41:31: #1 tags after filtering in treatment: 21440866 INFO @ Thu, 16 Apr 2020 00:41:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:31: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:32: #2 number of paired peaks: 128 WARNING @ Thu, 16 Apr 2020 00:41:32: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:32: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:32: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:41:32: #2 alternative fragment length(s) may be 3,55,346 bps INFO @ Thu, 16 Apr 2020 00:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.10_model.r WARNING @ Thu, 16 Apr 2020 00:41:32: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:41:32: #2 You may need to consider one of the other alternative d(s): 3,55,346 WARNING @ Thu, 16 Apr 2020 00:41:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:41:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:35: 17000000 INFO @ Thu, 16 Apr 2020 00:41:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:41: 18000000 INFO @ Thu, 16 Apr 2020 00:41:47: 19000000 INFO @ Thu, 16 Apr 2020 00:41:52: 20000000 INFO @ Thu, 16 Apr 2020 00:41:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.05_summits.bed INFO @ Thu, 16 Apr 2020 00:41:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11826 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:58: 21000000 INFO @ Thu, 16 Apr 2020 00:42:01: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:42:01: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:42:01: #1 total tags in treatment: 21440866 INFO @ Thu, 16 Apr 2020 00:42:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:42:01: #1 tags after filtering in treatment: 21440866 INFO @ Thu, 16 Apr 2020 00:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:42:01: #1 finished! INFO @ Thu, 16 Apr 2020 00:42:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:42:02: #2 number of paired peaks: 128 WARNING @ Thu, 16 Apr 2020 00:42:02: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Thu, 16 Apr 2020 00:42:02: start model_add_line... INFO @ Thu, 16 Apr 2020 00:42:03: start X-correlation... INFO @ Thu, 16 Apr 2020 00:42:03: end of X-cor INFO @ Thu, 16 Apr 2020 00:42:03: #2 finished! INFO @ Thu, 16 Apr 2020 00:42:03: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:42:03: #2 alternative fragment length(s) may be 3,55,346 bps INFO @ Thu, 16 Apr 2020 00:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.20_model.r WARNING @ Thu, 16 Apr 2020 00:42:03: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:42:03: #2 You may need to consider one of the other alternative d(s): 3,55,346 WARNING @ Thu, 16 Apr 2020 00:42:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:42:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:42:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.10_summits.bed INFO @ Thu, 16 Apr 2020 00:42:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7430 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592394/SRX2592394.20_summits.bed INFO @ Thu, 16 Apr 2020 00:43:01: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (758 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。