Job ID = 5720851 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,877,816 reads read : 34,877,816 reads written : 34,877,816 rm: cannot remove ‘[DSE]RR*’: 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: 00:11:13 34877816 reads; of these: 34877816 (100.00%) were unpaired; of these: 1183025 (3.39%) aligned 0 times 23369380 (67.00%) aligned exactly 1 time 10325411 (29.60%) aligned >1 times 96.61% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 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 16 files... [bam_rmdupse_core] 4966682 / 33694791 = 0.1474 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 02:38:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.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 02:38:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:38:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:38:44: 1000000 INFO @ Thu, 16 Apr 2020 02:38:50: 2000000 INFO @ Thu, 16 Apr 2020 02:38:57: 3000000 INFO @ Thu, 16 Apr 2020 02:39:04: 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 @ Thu, 16 Apr 2020 02:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.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 02:39:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:39:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:39:10: 5000000 INFO @ Thu, 16 Apr 2020 02:39:15: 1000000 INFO @ Thu, 16 Apr 2020 02:39:17: 6000000 INFO @ Thu, 16 Apr 2020 02:39:22: 2000000 INFO @ Thu, 16 Apr 2020 02:39:24: 7000000 INFO @ Thu, 16 Apr 2020 02:39:29: 3000000 INFO @ Thu, 16 Apr 2020 02:39:32: 8000000 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 02:39:36: 4000000 INFO @ Thu, 16 Apr 2020 02:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.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 02:39:37: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:39:37: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:39:39: 9000000 INFO @ Thu, 16 Apr 2020 02:39:44: 5000000 INFO @ Thu, 16 Apr 2020 02:39:45: 1000000 INFO @ Thu, 16 Apr 2020 02:39:46: 10000000 INFO @ Thu, 16 Apr 2020 02:39:51: 6000000 INFO @ Thu, 16 Apr 2020 02:39:52: 2000000 INFO @ Thu, 16 Apr 2020 02:39:53: 11000000 INFO @ Thu, 16 Apr 2020 02:39:59: 7000000 INFO @ Thu, 16 Apr 2020 02:39:59: 3000000 INFO @ Thu, 16 Apr 2020 02:40:01: 12000000 INFO @ Thu, 16 Apr 2020 02:40:06: 8000000 INFO @ Thu, 16 Apr 2020 02:40:07: 4000000 INFO @ Thu, 16 Apr 2020 02:40:08: 13000000 INFO @ Thu, 16 Apr 2020 02:40:14: 9000000 INFO @ Thu, 16 Apr 2020 02:40:14: 5000000 INFO @ Thu, 16 Apr 2020 02:40:15: 14000000 INFO @ Thu, 16 Apr 2020 02:40:21: 10000000 INFO @ Thu, 16 Apr 2020 02:40:21: 6000000 INFO @ Thu, 16 Apr 2020 02:40:22: 15000000 INFO @ Thu, 16 Apr 2020 02:40:28: 11000000 INFO @ Thu, 16 Apr 2020 02:40:28: 7000000 INFO @ Thu, 16 Apr 2020 02:40:29: 16000000 INFO @ Thu, 16 Apr 2020 02:40:35: 12000000 INFO @ Thu, 16 Apr 2020 02:40:35: 8000000 INFO @ Thu, 16 Apr 2020 02:40:36: 17000000 INFO @ Thu, 16 Apr 2020 02:40:42: 13000000 INFO @ Thu, 16 Apr 2020 02:40:42: 9000000 INFO @ Thu, 16 Apr 2020 02:40:44: 18000000 INFO @ Thu, 16 Apr 2020 02:40:49: 10000000 INFO @ Thu, 16 Apr 2020 02:40:49: 14000000 INFO @ Thu, 16 Apr 2020 02:40:51: 19000000 INFO @ Thu, 16 Apr 2020 02:40:56: 11000000 INFO @ Thu, 16 Apr 2020 02:40:57: 15000000 INFO @ Thu, 16 Apr 2020 02:40:58: 20000000 INFO @ Thu, 16 Apr 2020 02:41:03: 12000000 INFO @ Thu, 16 Apr 2020 02:41:04: 16000000 INFO @ Thu, 16 Apr 2020 02:41:05: 21000000 INFO @ Thu, 16 Apr 2020 02:41:10: 13000000 INFO @ Thu, 16 Apr 2020 02:41:11: 17000000 INFO @ Thu, 16 Apr 2020 02:41:12: 22000000 INFO @ Thu, 16 Apr 2020 02:41:17: 14000000 INFO @ Thu, 16 Apr 2020 02:41:18: 18000000 INFO @ Thu, 16 Apr 2020 02:41:20: 23000000 INFO @ Thu, 16 Apr 2020 02:41:24: 15000000 INFO @ Thu, 16 Apr 2020 02:41:25: 19000000 INFO @ Thu, 16 Apr 2020 02:41:27: 24000000 INFO @ Thu, 16 Apr 2020 02:41:31: 16000000 INFO @ Thu, 16 Apr 2020 02:41:33: 20000000 INFO @ Thu, 16 Apr 2020 02:41:34: 25000000 INFO @ Thu, 16 Apr 2020 02:41:38: 17000000 INFO @ Thu, 16 Apr 2020 02:41:40: 21000000 INFO @ Thu, 16 Apr 2020 02:41:42: 26000000 INFO @ Thu, 16 Apr 2020 02:41:46: 18000000 INFO @ Thu, 16 Apr 2020 02:41:47: 22000000 INFO @ Thu, 16 Apr 2020 02:41:50: 27000000 INFO @ Thu, 16 Apr 2020 02:41:53: 19000000 INFO @ Thu, 16 Apr 2020 02:41:54: 23000000 INFO @ Thu, 16 Apr 2020 02:41:58: 28000000 INFO @ Thu, 16 Apr 2020 02:42:00: 20000000 INFO @ Thu, 16 Apr 2020 02:42:02: 24000000 INFO @ Thu, 16 Apr 2020 02:42:03: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:42:03: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:42:03: #1 total tags in treatment: 28728109 INFO @ Thu, 16 Apr 2020 02:42:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:42:03: #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 02:42:04: #1 tags after filtering in treatment: 28728109 INFO @ Thu, 16 Apr 2020 02:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:42:04: #1 finished! INFO @ Thu, 16 Apr 2020 02:42:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:42:06: #2 number of paired peaks: 366 WARNING @ Thu, 16 Apr 2020 02:42:06: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Thu, 16 Apr 2020 02:42:06: start model_add_line... INFO @ Thu, 16 Apr 2020 02:42:06: start X-correlation... INFO @ Thu, 16 Apr 2020 02:42:06: end of X-cor INFO @ Thu, 16 Apr 2020 02:42:06: #2 finished! INFO @ Thu, 16 Apr 2020 02:42:06: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:42:06: #2 alternative fragment length(s) may be 1,27,45 bps INFO @ Thu, 16 Apr 2020 02:42:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.05_model.r WARNING @ Thu, 16 Apr 2020 02:42:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:42:06: #2 You may need to consider one of the other alternative d(s): 1,27,45 WARNING @ Thu, 16 Apr 2020 02:42:06: #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 02:42:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:42:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:42:08: 21000000 INFO @ Thu, 16 Apr 2020 02:42:09: 25000000 INFO @ Thu, 16 Apr 2020 02:42:15: 22000000 INFO @ Thu, 16 Apr 2020 02:42:16: 26000000 INFO @ Thu, 16 Apr 2020 02:42:22: 23000000 INFO @ Thu, 16 Apr 2020 02:42:23: 27000000 INFO @ Thu, 16 Apr 2020 02:42:29: 24000000 INFO @ Thu, 16 Apr 2020 02:42:31: 28000000 INFO @ Thu, 16 Apr 2020 02:42:36: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:42:36: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:42:36: #1 total tags in treatment: 28728109 INFO @ Thu, 16 Apr 2020 02:42:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:42:36: #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 02:42:36: #1 tags after filtering in treatment: 28728109 INFO @ Thu, 16 Apr 2020 02:42:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:42:36: #1 finished! INFO @ Thu, 16 Apr 2020 02:42:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:42:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:42:36: 25000000 INFO @ Thu, 16 Apr 2020 02:42:38: #2 number of paired peaks: 366 WARNING @ Thu, 16 Apr 2020 02:42:38: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Thu, 16 Apr 2020 02:42:38: start model_add_line... INFO @ Thu, 16 Apr 2020 02:42:38: start X-correlation... INFO @ Thu, 16 Apr 2020 02:42:38: end of X-cor INFO @ Thu, 16 Apr 2020 02:42:38: #2 finished! INFO @ Thu, 16 Apr 2020 02:42:38: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:42:38: #2 alternative fragment length(s) may be 1,27,45 bps INFO @ Thu, 16 Apr 2020 02:42:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.10_model.r WARNING @ Thu, 16 Apr 2020 02:42:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:42:38: #2 You may need to consider one of the other alternative d(s): 1,27,45 WARNING @ Thu, 16 Apr 2020 02:42:38: #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 02:42:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:42:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:42:43: 26000000 INFO @ Thu, 16 Apr 2020 02:42:50: 27000000 INFO @ Thu, 16 Apr 2020 02:42:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:42:57: 28000000 INFO @ Thu, 16 Apr 2020 02:43:02: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:43:02: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:43:02: #1 total tags in treatment: 28728109 INFO @ Thu, 16 Apr 2020 02:43:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:43:02: #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 02:43:02: #1 tags after filtering in treatment: 28728109 INFO @ Thu, 16 Apr 2020 02:43:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:43:02: #1 finished! INFO @ Thu, 16 Apr 2020 02:43:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:43:04: #2 number of paired peaks: 366 WARNING @ Thu, 16 Apr 2020 02:43:04: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Thu, 16 Apr 2020 02:43:04: start model_add_line... INFO @ Thu, 16 Apr 2020 02:43:04: start X-correlation... INFO @ Thu, 16 Apr 2020 02:43:04: end of X-cor INFO @ Thu, 16 Apr 2020 02:43:04: #2 finished! INFO @ Thu, 16 Apr 2020 02:43:04: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:43:04: #2 alternative fragment length(s) may be 1,27,45 bps INFO @ Thu, 16 Apr 2020 02:43:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.20_model.r WARNING @ Thu, 16 Apr 2020 02:43:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:43:04: #2 You may need to consider one of the other alternative d(s): 1,27,45 WARNING @ Thu, 16 Apr 2020 02:43:04: #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 02:43:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:43:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:43:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:43:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:43:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.05_summits.bed INFO @ Thu, 16 Apr 2020 02:43:12: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:43:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:43:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:43:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:43:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.10_summits.bed INFO @ Thu, 16 Apr 2020 02:43:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:43:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436044/SRX5436044.20_summits.bed INFO @ Thu, 16 Apr 2020 02:44:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。