Job ID = 5720763 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,538,178 reads read : 29,076,356 reads written : 14,538,178 reads 0-length : 14,538,178 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: 00:05:52 14538178 reads; of these: 14538178 (100.00%) were unpaired; of these: 1051525 (7.23%) aligned 0 times 9973913 (68.60%) aligned exactly 1 time 3512740 (24.16%) aligned >1 times 92.77% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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] 1134911 / 13486653 = 0.0842 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 01:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.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 01:31:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:31:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:31:38: 1000000 INFO @ Thu, 16 Apr 2020 01:31:44: 2000000 INFO @ Thu, 16 Apr 2020 01:31:51: 3000000 INFO @ Thu, 16 Apr 2020 01:31:57: 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 01:32:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.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 01:32:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:03: 5000000 INFO @ Thu, 16 Apr 2020 01:32:09: 1000000 INFO @ Thu, 16 Apr 2020 01:32:11: 6000000 INFO @ Thu, 16 Apr 2020 01:32:16: 2000000 INFO @ Thu, 16 Apr 2020 01:32:18: 7000000 INFO @ Thu, 16 Apr 2020 01:32:23: 3000000 INFO @ Thu, 16 Apr 2020 01:32:25: 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 01:32:30: 4000000 INFO @ Thu, 16 Apr 2020 01:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.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 01:32:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:32:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:32:32: 9000000 INFO @ Thu, 16 Apr 2020 01:32:38: 5000000 INFO @ Thu, 16 Apr 2020 01:32:40: 1000000 INFO @ Thu, 16 Apr 2020 01:32:40: 10000000 INFO @ Thu, 16 Apr 2020 01:32:46: 6000000 INFO @ Thu, 16 Apr 2020 01:32:48: 11000000 INFO @ Thu, 16 Apr 2020 01:32:48: 2000000 INFO @ Thu, 16 Apr 2020 01:32:54: 7000000 INFO @ Thu, 16 Apr 2020 01:32:56: 12000000 INFO @ Thu, 16 Apr 2020 01:32:56: 3000000 INFO @ Thu, 16 Apr 2020 01:32:59: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:32:59: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:32:59: #1 total tags in treatment: 12351742 INFO @ Thu, 16 Apr 2020 01:32:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:32:59: #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 01:32:59: #1 tags after filtering in treatment: 12351742 INFO @ Thu, 16 Apr 2020 01:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:32:59: #1 finished! INFO @ Thu, 16 Apr 2020 01:32:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:33:00: #2 number of paired peaks: 664 WARNING @ Thu, 16 Apr 2020 01:33:00: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Thu, 16 Apr 2020 01:33:00: start model_add_line... INFO @ Thu, 16 Apr 2020 01:33:00: start X-correlation... INFO @ Thu, 16 Apr 2020 01:33:00: end of X-cor INFO @ Thu, 16 Apr 2020 01:33:00: #2 finished! INFO @ Thu, 16 Apr 2020 01:33:00: #2 predicted fragment length is 83 bps INFO @ Thu, 16 Apr 2020 01:33:00: #2 alternative fragment length(s) may be 83 bps INFO @ Thu, 16 Apr 2020 01:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.05_model.r WARNING @ Thu, 16 Apr 2020 01:33:00: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:33:00: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Thu, 16 Apr 2020 01:33:00: #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 01:33:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:33:01: 8000000 INFO @ Thu, 16 Apr 2020 01:33:04: 4000000 INFO @ Thu, 16 Apr 2020 01:33:09: 9000000 INFO @ Thu, 16 Apr 2020 01:33:13: 5000000 INFO @ Thu, 16 Apr 2020 01:33:18: 10000000 INFO @ Thu, 16 Apr 2020 01:33:21: 6000000 INFO @ Thu, 16 Apr 2020 01:33:26: 11000000 INFO @ Thu, 16 Apr 2020 01:33:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:33:30: 7000000 INFO @ Thu, 16 Apr 2020 01:33:35: 12000000 INFO @ Thu, 16 Apr 2020 01:33:37: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:33:37: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:33:37: #1 total tags in treatment: 12351742 INFO @ Thu, 16 Apr 2020 01:33:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:33:37: #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 01:33:38: #1 tags after filtering in treatment: 12351742 INFO @ Thu, 16 Apr 2020 01:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:33:38: #1 finished! INFO @ Thu, 16 Apr 2020 01:33:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:33:38: 8000000 INFO @ Thu, 16 Apr 2020 01:33:39: #2 number of paired peaks: 664 WARNING @ Thu, 16 Apr 2020 01:33:39: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Thu, 16 Apr 2020 01:33:39: start model_add_line... INFO @ Thu, 16 Apr 2020 01:33:39: start X-correlation... INFO @ Thu, 16 Apr 2020 01:33:39: end of X-cor INFO @ Thu, 16 Apr 2020 01:33:39: #2 finished! INFO @ Thu, 16 Apr 2020 01:33:39: #2 predicted fragment length is 83 bps INFO @ Thu, 16 Apr 2020 01:33:39: #2 alternative fragment length(s) may be 83 bps INFO @ Thu, 16 Apr 2020 01:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.10_model.r WARNING @ Thu, 16 Apr 2020 01:33:39: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:33:39: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Thu, 16 Apr 2020 01:33:39: #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 01:33:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.05_summits.bed INFO @ Thu, 16 Apr 2020 01:33:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4382 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:33:46: 9000000 INFO @ Thu, 16 Apr 2020 01:33:54: 10000000 INFO @ Thu, 16 Apr 2020 01:34:02: 11000000 INFO @ Thu, 16 Apr 2020 01:34:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:34:11: 12000000 INFO @ Thu, 16 Apr 2020 01:34:14: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 01:34:14: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 01:34:14: #1 total tags in treatment: 12351742 INFO @ Thu, 16 Apr 2020 01:34:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:34:14: #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 01:34:14: #1 tags after filtering in treatment: 12351742 INFO @ Thu, 16 Apr 2020 01:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:34:14: #1 finished! INFO @ Thu, 16 Apr 2020 01:34:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:34:15: #2 number of paired peaks: 664 WARNING @ Thu, 16 Apr 2020 01:34:15: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Thu, 16 Apr 2020 01:34:15: start model_add_line... INFO @ Thu, 16 Apr 2020 01:34:15: start X-correlation... INFO @ Thu, 16 Apr 2020 01:34:15: end of X-cor INFO @ Thu, 16 Apr 2020 01:34:15: #2 finished! INFO @ Thu, 16 Apr 2020 01:34:15: #2 predicted fragment length is 83 bps INFO @ Thu, 16 Apr 2020 01:34:15: #2 alternative fragment length(s) may be 83 bps INFO @ Thu, 16 Apr 2020 01:34:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.20_model.r WARNING @ Thu, 16 Apr 2020 01:34:15: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:34:15: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Thu, 16 Apr 2020 01:34:15: #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 01:34:15: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:34:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.10_summits.bed INFO @ Thu, 16 Apr 2020 01:34:19: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2038 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:34:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:34:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:34:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:34:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227000/SRX5227000.20_summits.bed INFO @ Thu, 16 Apr 2020 01:34:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (773 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。