Job ID = 5720767 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,388,222 reads read : 40,776,444 reads written : 20,388,222 reads 0-length : 20,388,222 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: 00:09:10 20388222 reads; of these: 20388222 (100.00%) were unpaired; of these: 1477326 (7.25%) aligned 0 times 12633279 (61.96%) aligned exactly 1 time 6277617 (30.79%) aligned >1 times 92.75% overall alignment rate Time searching: 00:09:10 Overall time: 00:09:10 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 8 files... [bam_rmdupse_core] 3327485 / 18910896 = 0.1760 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 01:40:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.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 01:40:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:40:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:41:04: 1000000 INFO @ Thu, 16 Apr 2020 01:41:09: 2000000 INFO @ Thu, 16 Apr 2020 01:41:15: 3000000 INFO @ Thu, 16 Apr 2020 01:41:21: 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 01:41:26: 5000000 INFO @ Thu, 16 Apr 2020 01:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.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 01:41:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:41:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:41:32: 6000000 INFO @ Thu, 16 Apr 2020 01:41:34: 1000000 INFO @ Thu, 16 Apr 2020 01:41:39: 7000000 INFO @ Thu, 16 Apr 2020 01:41:40: 2000000 INFO @ Thu, 16 Apr 2020 01:41:45: 8000000 INFO @ Thu, 16 Apr 2020 01:41:46: 3000000 INFO @ Thu, 16 Apr 2020 01:41:51: 9000000 INFO @ Thu, 16 Apr 2020 01:41:52: 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 01:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.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 01:41:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:41:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:41:57: 10000000 INFO @ Thu, 16 Apr 2020 01:41:59: 5000000 INFO @ Thu, 16 Apr 2020 01:42:03: 1000000 INFO @ Thu, 16 Apr 2020 01:42:04: 11000000 INFO @ Thu, 16 Apr 2020 01:42:05: 6000000 INFO @ Thu, 16 Apr 2020 01:42:09: 2000000 INFO @ Thu, 16 Apr 2020 01:42:10: 12000000 INFO @ Thu, 16 Apr 2020 01:42:11: 7000000 INFO @ Thu, 16 Apr 2020 01:42:16: 3000000 INFO @ Thu, 16 Apr 2020 01:42:17: 13000000 INFO @ Thu, 16 Apr 2020 01:42:18: 8000000 INFO @ Thu, 16 Apr 2020 01:42:22: 4000000 INFO @ Thu, 16 Apr 2020 01:42:23: 14000000 INFO @ Thu, 16 Apr 2020 01:42:24: 9000000 INFO @ Thu, 16 Apr 2020 01:42:28: 5000000 INFO @ Thu, 16 Apr 2020 01:42:29: 15000000 INFO @ Thu, 16 Apr 2020 01:42:30: 10000000 INFO @ Thu, 16 Apr 2020 01:42:33: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:42:33: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:42:33: #1 total tags in treatment: 15583411 INFO @ Thu, 16 Apr 2020 01:42:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:42:33: #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 01:42:33: #1 tags after filtering in treatment: 15583411 INFO @ Thu, 16 Apr 2020 01:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:42:33: #1 finished! INFO @ Thu, 16 Apr 2020 01:42:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:42:34: #2 number of paired peaks: 943 WARNING @ Thu, 16 Apr 2020 01:42:34: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Thu, 16 Apr 2020 01:42:34: start model_add_line... INFO @ Thu, 16 Apr 2020 01:42:34: start X-correlation... INFO @ Thu, 16 Apr 2020 01:42:34: end of X-cor INFO @ Thu, 16 Apr 2020 01:42:34: #2 finished! INFO @ Thu, 16 Apr 2020 01:42:34: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 01:42:34: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 01:42:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.05_model.r WARNING @ Thu, 16 Apr 2020 01:42:34: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:42:34: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 16 Apr 2020 01:42:34: #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 01:42:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:42:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:42:34: 6000000 INFO @ Thu, 16 Apr 2020 01:42:36: 11000000 INFO @ Thu, 16 Apr 2020 01:42:41: 7000000 INFO @ Thu, 16 Apr 2020 01:42:43: 12000000 INFO @ Thu, 16 Apr 2020 01:42:47: 8000000 INFO @ Thu, 16 Apr 2020 01:42:49: 13000000 INFO @ Thu, 16 Apr 2020 01:42:53: 9000000 INFO @ Thu, 16 Apr 2020 01:42:55: 14000000 INFO @ Thu, 16 Apr 2020 01:43:00: 10000000 INFO @ Thu, 16 Apr 2020 01:43:01: 15000000 INFO @ Thu, 16 Apr 2020 01:43:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:43:05: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:43:05: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:43:05: #1 total tags in treatment: 15583411 INFO @ Thu, 16 Apr 2020 01:43:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:43:05: #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 01:43:05: #1 tags after filtering in treatment: 15583411 INFO @ Thu, 16 Apr 2020 01:43:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:43:05: #1 finished! INFO @ Thu, 16 Apr 2020 01:43:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:43:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:43:06: 11000000 INFO @ Thu, 16 Apr 2020 01:43:06: #2 number of paired peaks: 943 WARNING @ Thu, 16 Apr 2020 01:43:06: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Thu, 16 Apr 2020 01:43:06: start model_add_line... INFO @ Thu, 16 Apr 2020 01:43:06: start X-correlation... INFO @ Thu, 16 Apr 2020 01:43:07: end of X-cor INFO @ Thu, 16 Apr 2020 01:43:07: #2 finished! INFO @ Thu, 16 Apr 2020 01:43:07: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 01:43:07: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 01:43:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.10_model.r WARNING @ Thu, 16 Apr 2020 01:43:07: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:43:07: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 16 Apr 2020 01:43:07: #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 01:43:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:43:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:43:12: 12000000 INFO @ Thu, 16 Apr 2020 01:43:18: 13000000 INFO @ Thu, 16 Apr 2020 01:43:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:43:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:43:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.05_summits.bed INFO @ Thu, 16 Apr 2020 01:43:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5051 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:43:24: 14000000 INFO @ Thu, 16 Apr 2020 01:43:30: 15000000 INFO @ Thu, 16 Apr 2020 01:43:33: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:43:33: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:43:33: #1 total tags in treatment: 15583411 INFO @ Thu, 16 Apr 2020 01:43:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:43:33: #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 01:43:34: #1 tags after filtering in treatment: 15583411 INFO @ Thu, 16 Apr 2020 01:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:43:34: #1 finished! INFO @ Thu, 16 Apr 2020 01:43:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:43:35: #2 number of paired peaks: 943 WARNING @ Thu, 16 Apr 2020 01:43:35: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Thu, 16 Apr 2020 01:43:35: start model_add_line... INFO @ Thu, 16 Apr 2020 01:43:35: start X-correlation... INFO @ Thu, 16 Apr 2020 01:43:35: end of X-cor INFO @ Thu, 16 Apr 2020 01:43:35: #2 finished! INFO @ Thu, 16 Apr 2020 01:43:35: #2 predicted fragment length is 90 bps INFO @ Thu, 16 Apr 2020 01:43:35: #2 alternative fragment length(s) may be 90 bps INFO @ Thu, 16 Apr 2020 01:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.20_model.r WARNING @ Thu, 16 Apr 2020 01:43:35: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:43:35: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Thu, 16 Apr 2020 01:43:35: #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 01:43:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:43:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:43:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:43:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.10_summits.bed INFO @ Thu, 16 Apr 2020 01:43:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3056 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:44:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:44:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227004/SRX5227004.20_summits.bed INFO @ Thu, 16 Apr 2020 01:44:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1583 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。