Job ID = 5720868 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 44,412,060 reads read : 44,412,060 reads written : 44,412,060 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR8637386.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:42 44412060 reads; of these: 44412060 (100.00%) were unpaired; of these: 1965465 (4.43%) aligned 0 times 29508605 (66.44%) aligned exactly 1 time 12937990 (29.13%) aligned >1 times 95.57% overall alignment rate Time searching: 00:15:43 Overall time: 00:15:43 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 20 files... [bam_rmdupse_core] 7814687 / 42446595 = 0.1841 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 02:54:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.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 02:54:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:54:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:54:55: 1000000 INFO @ Thu, 16 Apr 2020 02:55:01: 2000000 INFO @ Thu, 16 Apr 2020 02:55:07: 3000000 INFO @ Thu, 16 Apr 2020 02:55:13: 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 02:55:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.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 02:55:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:55:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:55:19: 5000000 INFO @ Thu, 16 Apr 2020 02:55:25: 1000000 INFO @ Thu, 16 Apr 2020 02:55:25: 6000000 INFO @ Thu, 16 Apr 2020 02:55:31: 2000000 INFO @ Thu, 16 Apr 2020 02:55:31: 7000000 INFO @ Thu, 16 Apr 2020 02:55:38: 8000000 INFO @ Thu, 16 Apr 2020 02:55:38: 3000000 INFO @ Thu, 16 Apr 2020 02:55:44: 9000000 INFO @ Thu, 16 Apr 2020 02:55:44: 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 @ Thu, 16 Apr 2020 02:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.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 02:55:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:55:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:55:50: 10000000 INFO @ Thu, 16 Apr 2020 02:55:50: 5000000 INFO @ Thu, 16 Apr 2020 02:55:55: 1000000 INFO @ Thu, 16 Apr 2020 02:55:56: 11000000 INFO @ Thu, 16 Apr 2020 02:55:57: 6000000 INFO @ Thu, 16 Apr 2020 02:56:01: 2000000 INFO @ Thu, 16 Apr 2020 02:56:02: 12000000 INFO @ Thu, 16 Apr 2020 02:56:03: 7000000 INFO @ Thu, 16 Apr 2020 02:56:08: 3000000 INFO @ Thu, 16 Apr 2020 02:56:09: 13000000 INFO @ Thu, 16 Apr 2020 02:56:10: 8000000 INFO @ Thu, 16 Apr 2020 02:56:14: 4000000 INFO @ Thu, 16 Apr 2020 02:56:15: 14000000 INFO @ Thu, 16 Apr 2020 02:56:16: 9000000 INFO @ Thu, 16 Apr 2020 02:56:21: 5000000 INFO @ Thu, 16 Apr 2020 02:56:22: 15000000 INFO @ Thu, 16 Apr 2020 02:56:22: 10000000 INFO @ Thu, 16 Apr 2020 02:56:27: 6000000 INFO @ Thu, 16 Apr 2020 02:56:28: 16000000 INFO @ Thu, 16 Apr 2020 02:56:29: 11000000 INFO @ Thu, 16 Apr 2020 02:56:33: 7000000 INFO @ Thu, 16 Apr 2020 02:56:35: 17000000 INFO @ Thu, 16 Apr 2020 02:56:35: 12000000 INFO @ Thu, 16 Apr 2020 02:56:39: 8000000 INFO @ Thu, 16 Apr 2020 02:56:41: 18000000 INFO @ Thu, 16 Apr 2020 02:56:41: 13000000 INFO @ Thu, 16 Apr 2020 02:56:46: 9000000 INFO @ Thu, 16 Apr 2020 02:56:48: 19000000 INFO @ Thu, 16 Apr 2020 02:56:48: 14000000 INFO @ Thu, 16 Apr 2020 02:56:52: 10000000 INFO @ Thu, 16 Apr 2020 02:56:54: 20000000 INFO @ Thu, 16 Apr 2020 02:56:54: 15000000 INFO @ Thu, 16 Apr 2020 02:56:58: 11000000 INFO @ Thu, 16 Apr 2020 02:57:00: 21000000 INFO @ Thu, 16 Apr 2020 02:57:01: 16000000 INFO @ Thu, 16 Apr 2020 02:57:04: 12000000 INFO @ Thu, 16 Apr 2020 02:57:07: 22000000 INFO @ Thu, 16 Apr 2020 02:57:07: 17000000 INFO @ Thu, 16 Apr 2020 02:57:11: 13000000 INFO @ Thu, 16 Apr 2020 02:57:13: 23000000 INFO @ Thu, 16 Apr 2020 02:57:14: 18000000 INFO @ Thu, 16 Apr 2020 02:57:17: 14000000 INFO @ Thu, 16 Apr 2020 02:57:20: 24000000 INFO @ Thu, 16 Apr 2020 02:57:20: 19000000 INFO @ Thu, 16 Apr 2020 02:57:24: 15000000 INFO @ Thu, 16 Apr 2020 02:57:26: 25000000 INFO @ Thu, 16 Apr 2020 02:57:26: 20000000 INFO @ Thu, 16 Apr 2020 02:57:30: 16000000 INFO @ Thu, 16 Apr 2020 02:57:33: 21000000 INFO @ Thu, 16 Apr 2020 02:57:33: 26000000 INFO @ Thu, 16 Apr 2020 02:57:36: 17000000 INFO @ Thu, 16 Apr 2020 02:57:39: 22000000 INFO @ Thu, 16 Apr 2020 02:57:39: 27000000 INFO @ Thu, 16 Apr 2020 02:57:43: 18000000 INFO @ Thu, 16 Apr 2020 02:57:46: 23000000 INFO @ Thu, 16 Apr 2020 02:57:46: 28000000 INFO @ Thu, 16 Apr 2020 02:57:49: 19000000 INFO @ Thu, 16 Apr 2020 02:57:52: 24000000 INFO @ Thu, 16 Apr 2020 02:57:53: 29000000 INFO @ Thu, 16 Apr 2020 02:57:56: 20000000 INFO @ Thu, 16 Apr 2020 02:57:59: 25000000 INFO @ Thu, 16 Apr 2020 02:57:59: 30000000 INFO @ Thu, 16 Apr 2020 02:58:02: 21000000 INFO @ Thu, 16 Apr 2020 02:58:05: 26000000 INFO @ Thu, 16 Apr 2020 02:58:06: 31000000 INFO @ Thu, 16 Apr 2020 02:58:09: 22000000 INFO @ Thu, 16 Apr 2020 02:58:12: 27000000 INFO @ Thu, 16 Apr 2020 02:58:12: 32000000 INFO @ Thu, 16 Apr 2020 02:58:15: 23000000 INFO @ Thu, 16 Apr 2020 02:58:19: 28000000 INFO @ Thu, 16 Apr 2020 02:58:19: 33000000 INFO @ Thu, 16 Apr 2020 02:58:22: 24000000 INFO @ Thu, 16 Apr 2020 02:58:25: 29000000 INFO @ Thu, 16 Apr 2020 02:58:25: 34000000 INFO @ Thu, 16 Apr 2020 02:58:29: 25000000 INFO @ Thu, 16 Apr 2020 02:58:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:58:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:58:30: #1 total tags in treatment: 34631908 INFO @ Thu, 16 Apr 2020 02:58:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:58:30: #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 02:58:30: #1 tags after filtering in treatment: 34631908 INFO @ Thu, 16 Apr 2020 02:58:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:58:30: #1 finished! INFO @ Thu, 16 Apr 2020 02:58:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:58:32: 30000000 INFO @ Thu, 16 Apr 2020 02:58:32: #2 number of paired peaks: 253 WARNING @ Thu, 16 Apr 2020 02:58:32: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Thu, 16 Apr 2020 02:58:32: start model_add_line... INFO @ Thu, 16 Apr 2020 02:58:33: start X-correlation... INFO @ Thu, 16 Apr 2020 02:58:33: end of X-cor INFO @ Thu, 16 Apr 2020 02:58:33: #2 finished! INFO @ Thu, 16 Apr 2020 02:58:33: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:58:33: #2 alternative fragment length(s) may be 1,19 bps INFO @ Thu, 16 Apr 2020 02:58:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.05_model.r WARNING @ Thu, 16 Apr 2020 02:58:33: #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 02:58:33: #2 You may need to consider one of the other alternative d(s): 1,19 WARNING @ Thu, 16 Apr 2020 02:58:33: #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 02:58:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:58:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:58:36: 26000000 INFO @ Thu, 16 Apr 2020 02:58:38: 31000000 INFO @ Thu, 16 Apr 2020 02:58:42: 27000000 INFO @ Thu, 16 Apr 2020 02:58:45: 32000000 INFO @ Thu, 16 Apr 2020 02:58:49: 28000000 INFO @ Thu, 16 Apr 2020 02:58:51: 33000000 INFO @ Thu, 16 Apr 2020 02:58:56: 29000000 INFO @ Thu, 16 Apr 2020 02:58:58: 34000000 INFO @ Thu, 16 Apr 2020 02:59:02: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:59:02: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:59:02: #1 total tags in treatment: 34631908 INFO @ Thu, 16 Apr 2020 02:59:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:59:02: #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 02:59:02: 30000000 INFO @ Thu, 16 Apr 2020 02:59:03: #1 tags after filtering in treatment: 34631908 INFO @ Thu, 16 Apr 2020 02:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:59:03: #1 finished! INFO @ Thu, 16 Apr 2020 02:59:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:59:05: #2 number of paired peaks: 253 WARNING @ Thu, 16 Apr 2020 02:59:05: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Thu, 16 Apr 2020 02:59:05: start model_add_line... INFO @ Thu, 16 Apr 2020 02:59:05: start X-correlation... INFO @ Thu, 16 Apr 2020 02:59:05: end of X-cor INFO @ Thu, 16 Apr 2020 02:59:05: #2 finished! INFO @ Thu, 16 Apr 2020 02:59:05: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:59:05: #2 alternative fragment length(s) may be 1,19 bps INFO @ Thu, 16 Apr 2020 02:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.10_model.r WARNING @ Thu, 16 Apr 2020 02:59:05: #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 02:59:05: #2 You may need to consider one of the other alternative d(s): 1,19 WARNING @ Thu, 16 Apr 2020 02:59:05: #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 02:59:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:59:08: 31000000 INFO @ Thu, 16 Apr 2020 02:59:14: 32000000 INFO @ Thu, 16 Apr 2020 02:59:21: 33000000 INFO @ Thu, 16 Apr 2020 02:59:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:59:27: 34000000 INFO @ Thu, 16 Apr 2020 02:59:31: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 02:59:31: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 02:59:31: #1 total tags in treatment: 34631908 INFO @ Thu, 16 Apr 2020 02:59:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:59:31: #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 02:59:32: #1 tags after filtering in treatment: 34631908 INFO @ Thu, 16 Apr 2020 02:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 02:59:32: #1 finished! INFO @ Thu, 16 Apr 2020 02:59:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:59:34: #2 number of paired peaks: 253 WARNING @ Thu, 16 Apr 2020 02:59:34: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Thu, 16 Apr 2020 02:59:34: start model_add_line... INFO @ Thu, 16 Apr 2020 02:59:34: start X-correlation... INFO @ Thu, 16 Apr 2020 02:59:34: end of X-cor INFO @ Thu, 16 Apr 2020 02:59:34: #2 finished! INFO @ Thu, 16 Apr 2020 02:59:34: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 02:59:34: #2 alternative fragment length(s) may be 1,19 bps INFO @ Thu, 16 Apr 2020 02:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.20_model.r WARNING @ Thu, 16 Apr 2020 02:59:34: #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 02:59:34: #2 You may need to consider one of the other alternative d(s): 1,19 WARNING @ Thu, 16 Apr 2020 02:59:34: #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 02:59:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.05_summits.bed INFO @ Thu, 16 Apr 2020 02:59:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:59:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:00:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:00:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:00:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.10_summits.bed INFO @ Thu, 16 Apr 2020 03:00:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:00:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:00:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:00:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5436054/SRX5436054.20_summits.bed INFO @ Thu, 16 Apr 2020 03:00:51: Done! pass1 - making usageList (0 chroms): 1 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。