Job ID = 6529992 SRX = SRX5775936 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:11:56 34228787 reads; of these: 34228787 (100.00%) were unpaired; of these: 960871 (2.81%) aligned 0 times 24126314 (70.49%) aligned exactly 1 time 9141602 (26.71%) aligned >1 times 97.19% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 13735640 / 33267916 = 0.4129 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 @ Tue, 30 Jun 2020 03:15:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.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 @ Tue, 30 Jun 2020 03:15:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:20: 1000000 INFO @ Tue, 30 Jun 2020 03:15:26: 2000000 INFO @ Tue, 30 Jun 2020 03:15:32: 3000000 INFO @ Tue, 30 Jun 2020 03:15:37: 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 @ Tue, 30 Jun 2020 03:15:43: 5000000 INFO @ Tue, 30 Jun 2020 03:15:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.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 @ Tue, 30 Jun 2020 03:15:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:48: 6000000 INFO @ Tue, 30 Jun 2020 03:15:49: 1000000 INFO @ Tue, 30 Jun 2020 03:15:54: 7000000 INFO @ Tue, 30 Jun 2020 03:15:54: 2000000 INFO @ Tue, 30 Jun 2020 03:16:00: 8000000 INFO @ Tue, 30 Jun 2020 03:16:00: 3000000 INFO @ Tue, 30 Jun 2020 03:16:05: 9000000 INFO @ Tue, 30 Jun 2020 03:16:06: 4000000 INFO @ Tue, 30 Jun 2020 03:16:11: 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 @ Tue, 30 Jun 2020 03:16:12: 5000000 INFO @ Tue, 30 Jun 2020 03:16:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.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 @ Tue, 30 Jun 2020 03:16:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:16:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:16:17: 11000000 INFO @ Tue, 30 Jun 2020 03:16:17: 6000000 INFO @ Tue, 30 Jun 2020 03:16:19: 1000000 INFO @ Tue, 30 Jun 2020 03:16:23: 12000000 INFO @ Tue, 30 Jun 2020 03:16:23: 7000000 INFO @ Tue, 30 Jun 2020 03:16:25: 2000000 INFO @ Tue, 30 Jun 2020 03:16:28: 13000000 INFO @ Tue, 30 Jun 2020 03:16:29: 8000000 INFO @ Tue, 30 Jun 2020 03:16:30: 3000000 INFO @ Tue, 30 Jun 2020 03:16:34: 14000000 INFO @ Tue, 30 Jun 2020 03:16:34: 9000000 INFO @ Tue, 30 Jun 2020 03:16:36: 4000000 INFO @ Tue, 30 Jun 2020 03:16:40: 15000000 INFO @ Tue, 30 Jun 2020 03:16:40: 10000000 INFO @ Tue, 30 Jun 2020 03:16:42: 5000000 INFO @ Tue, 30 Jun 2020 03:16:46: 16000000 INFO @ Tue, 30 Jun 2020 03:16:46: 11000000 INFO @ Tue, 30 Jun 2020 03:16:48: 6000000 INFO @ Tue, 30 Jun 2020 03:16:51: 17000000 INFO @ Tue, 30 Jun 2020 03:16:51: 12000000 INFO @ Tue, 30 Jun 2020 03:16:53: 7000000 INFO @ Tue, 30 Jun 2020 03:16:57: 18000000 INFO @ Tue, 30 Jun 2020 03:16:57: 13000000 INFO @ Tue, 30 Jun 2020 03:16:59: 8000000 INFO @ Tue, 30 Jun 2020 03:17:03: 19000000 INFO @ Tue, 30 Jun 2020 03:17:03: 14000000 INFO @ Tue, 30 Jun 2020 03:17:05: 9000000 INFO @ Tue, 30 Jun 2020 03:17:06: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:17:06: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:17:06: #1 total tags in treatment: 19532276 INFO @ Tue, 30 Jun 2020 03:17:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:17:07: #1 tags after filtering in treatment: 19532276 INFO @ Tue, 30 Jun 2020 03:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:07: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:08: #2 number of paired peaks: 742 WARNING @ Tue, 30 Jun 2020 03:17:08: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:08: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:08: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:08: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:08: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:08: #2 predicted fragment length is 60 bps INFO @ Tue, 30 Jun 2020 03:17:08: #2 alternative fragment length(s) may be 3,60 bps INFO @ Tue, 30 Jun 2020 03:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.05_model.r WARNING @ Tue, 30 Jun 2020 03:17:08: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:08: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Tue, 30 Jun 2020 03:17:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:17:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:09: 15000000 INFO @ Tue, 30 Jun 2020 03:17:10: 10000000 INFO @ Tue, 30 Jun 2020 03:17:15: 16000000 INFO @ Tue, 30 Jun 2020 03:17:16: 11000000 INFO @ Tue, 30 Jun 2020 03:17:20: 17000000 INFO @ Tue, 30 Jun 2020 03:17:22: 12000000 INFO @ Tue, 30 Jun 2020 03:17:26: 18000000 INFO @ Tue, 30 Jun 2020 03:17:28: 13000000 INFO @ Tue, 30 Jun 2020 03:17:32: 19000000 INFO @ Tue, 30 Jun 2020 03:17:33: 14000000 INFO @ Tue, 30 Jun 2020 03:17:35: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:17:35: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:17:35: #1 total tags in treatment: 19532276 INFO @ Tue, 30 Jun 2020 03:17:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:17:35: #1 tags after filtering in treatment: 19532276 INFO @ Tue, 30 Jun 2020 03:17:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:35: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:37: #2 number of paired peaks: 742 WARNING @ Tue, 30 Jun 2020 03:17:37: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:37: #2 predicted fragment length is 60 bps INFO @ Tue, 30 Jun 2020 03:17:37: #2 alternative fragment length(s) may be 3,60 bps INFO @ Tue, 30 Jun 2020 03:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.10_model.r WARNING @ Tue, 30 Jun 2020 03:17:37: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:37: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Tue, 30 Jun 2020 03:17:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:17:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:39: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:17:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:17:45: 16000000 INFO @ Tue, 30 Jun 2020 03:17:50: 17000000 INFO @ Tue, 30 Jun 2020 03:17:56: 18000000 INFO @ Tue, 30 Jun 2020 03:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.05_summits.bed INFO @ Tue, 30 Jun 2020 03:18:00: Done! pass1 - making usageList (831 chroms): 1 millis pass2 - checking and writing primary data (2876 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:18:01: 19000000 INFO @ Tue, 30 Jun 2020 03:18:04: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:18:04: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:18:04: #1 total tags in treatment: 19532276 INFO @ Tue, 30 Jun 2020 03:18:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:18:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:18:05: #1 tags after filtering in treatment: 19532276 INFO @ Tue, 30 Jun 2020 03:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:18:05: #1 finished! INFO @ Tue, 30 Jun 2020 03:18:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:18:06: #2 number of paired peaks: 742 WARNING @ Tue, 30 Jun 2020 03:18:06: Fewer paired peaks (742) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 742 pairs to build model! INFO @ Tue, 30 Jun 2020 03:18:06: start model_add_line... INFO @ Tue, 30 Jun 2020 03:18:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:18:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:18:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:18:06: #2 predicted fragment length is 60 bps INFO @ Tue, 30 Jun 2020 03:18:06: #2 alternative fragment length(s) may be 3,60 bps INFO @ Tue, 30 Jun 2020 03:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.20_model.r WARNING @ Tue, 30 Jun 2020 03:18:06: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:18:06: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Tue, 30 Jun 2020 03:18:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:18:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:18:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.10_summits.bed INFO @ Tue, 30 Jun 2020 03:18:28: Done! pass1 - making usageList (695 chroms): 1 millis pass2 - checking and writing primary data (2095 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:18:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:18:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775936/SRX5775936.20_summits.bed INFO @ Tue, 30 Jun 2020 03:18:59: Done! pass1 - making usageList (535 chroms): 2 millis pass2 - checking and writing primary data (1465 records, 4 fields): 15 millis CompletedMACS2peakCalling