Job ID = 6626455 SRX = SRX1532033 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18135121 spots for SRR3103383/SRR3103383.sra Written 18135121 spots for SRR3103383/SRR3103383.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626610 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:46 18135121 reads; of these: 18135121 (100.00%) were unpaired; of these: 1084792 (5.98%) aligned 0 times 11759236 (64.84%) aligned exactly 1 time 5291093 (29.18%) aligned >1 times 94.02% overall alignment rate Time searching: 00:05:46 Overall time: 00:05:46 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] 1988309 / 17050329 = 0.1166 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, 14 Jul 2020 07:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.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, 14 Jul 2020 07:14:07: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:14:07: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:14:15: 1000000 INFO @ Tue, 14 Jul 2020 07:14:22: 2000000 INFO @ Tue, 14 Jul 2020 07:14:29: 3000000 INFO @ Tue, 14 Jul 2020 07:14:36: 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, 14 Jul 2020 07:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.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, 14 Jul 2020 07:14:37: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:14:37: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:14:43: 5000000 INFO @ Tue, 14 Jul 2020 07:14:45: 1000000 INFO @ Tue, 14 Jul 2020 07:14:51: 6000000 INFO @ Tue, 14 Jul 2020 07:14:53: 2000000 INFO @ Tue, 14 Jul 2020 07:14:58: 7000000 INFO @ Tue, 14 Jul 2020 07:15:00: 3000000 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, 14 Jul 2020 07:15:06: 8000000 INFO @ Tue, 14 Jul 2020 07:15:07: 4000000 INFO @ Tue, 14 Jul 2020 07:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.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, 14 Jul 2020 07:15:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:15:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:15:14: 9000000 INFO @ Tue, 14 Jul 2020 07:15:15: 5000000 INFO @ Tue, 14 Jul 2020 07:15:16: 1000000 INFO @ Tue, 14 Jul 2020 07:15:22: 10000000 INFO @ Tue, 14 Jul 2020 07:15:22: 6000000 INFO @ Tue, 14 Jul 2020 07:15:24: 2000000 INFO @ Tue, 14 Jul 2020 07:15:30: 11000000 INFO @ Tue, 14 Jul 2020 07:15:30: 7000000 INFO @ Tue, 14 Jul 2020 07:15:32: 3000000 INFO @ Tue, 14 Jul 2020 07:15:38: 8000000 INFO @ Tue, 14 Jul 2020 07:15:38: 12000000 INFO @ Tue, 14 Jul 2020 07:15:40: 4000000 INFO @ Tue, 14 Jul 2020 07:15:45: 9000000 INFO @ Tue, 14 Jul 2020 07:15:46: 13000000 INFO @ Tue, 14 Jul 2020 07:15:48: 5000000 INFO @ Tue, 14 Jul 2020 07:15:53: 10000000 INFO @ Tue, 14 Jul 2020 07:15:54: 14000000 INFO @ Tue, 14 Jul 2020 07:15:56: 6000000 INFO @ Tue, 14 Jul 2020 07:16:00: 11000000 INFO @ Tue, 14 Jul 2020 07:16:02: 15000000 INFO @ Tue, 14 Jul 2020 07:16:03: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:16:03: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:16:03: #1 total tags in treatment: 15062020 INFO @ Tue, 14 Jul 2020 07:16:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:16:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:16:03: #1 tags after filtering in treatment: 15062020 INFO @ Tue, 14 Jul 2020 07:16:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:16:03: #1 finished! INFO @ Tue, 14 Jul 2020 07:16:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:16:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:16:04: 7000000 INFO @ Tue, 14 Jul 2020 07:16:04: #2 number of paired peaks: 793 WARNING @ Tue, 14 Jul 2020 07:16:04: Fewer paired peaks (793) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 793 pairs to build model! INFO @ Tue, 14 Jul 2020 07:16:04: start model_add_line... INFO @ Tue, 14 Jul 2020 07:16:04: start X-correlation... INFO @ Tue, 14 Jul 2020 07:16:04: end of X-cor INFO @ Tue, 14 Jul 2020 07:16:04: #2 finished! INFO @ Tue, 14 Jul 2020 07:16:04: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 07:16:04: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 14 Jul 2020 07:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.05_model.r WARNING @ Tue, 14 Jul 2020 07:16:04: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:16:04: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 14 Jul 2020 07:16:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:16:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:16:08: 12000000 INFO @ Tue, 14 Jul 2020 07:16:12: 8000000 INFO @ Tue, 14 Jul 2020 07:16:15: 13000000 INFO @ Tue, 14 Jul 2020 07:16:20: 9000000 INFO @ Tue, 14 Jul 2020 07:16:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:16:27: 10000000 INFO @ Tue, 14 Jul 2020 07:16:30: 15000000 INFO @ Tue, 14 Jul 2020 07:16:31: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:16:31: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:16:31: #1 total tags in treatment: 15062020 INFO @ Tue, 14 Jul 2020 07:16:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:16:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:16:31: #1 tags after filtering in treatment: 15062020 INFO @ Tue, 14 Jul 2020 07:16:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:16:31: #1 finished! INFO @ Tue, 14 Jul 2020 07:16:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:16:32: #2 number of paired peaks: 793 WARNING @ Tue, 14 Jul 2020 07:16:32: Fewer paired peaks (793) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 793 pairs to build model! INFO @ Tue, 14 Jul 2020 07:16:32: start model_add_line... INFO @ Tue, 14 Jul 2020 07:16:32: start X-correlation... INFO @ Tue, 14 Jul 2020 07:16:32: end of X-cor INFO @ Tue, 14 Jul 2020 07:16:32: #2 finished! INFO @ Tue, 14 Jul 2020 07:16:32: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 07:16:32: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 14 Jul 2020 07:16:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.10_model.r WARNING @ Tue, 14 Jul 2020 07:16:32: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:16:32: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 14 Jul 2020 07:16:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:16:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:16:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:16:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:16:35: 11000000 INFO @ Tue, 14 Jul 2020 07:16:42: 12000000 INFO @ Tue, 14 Jul 2020 07:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:16:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.05_summits.bed INFO @ Tue, 14 Jul 2020 07:16:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3741 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:16:49: 13000000 INFO @ Tue, 14 Jul 2020 07:16:57: 14000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:17:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:17:04: 15000000 INFO @ Tue, 14 Jul 2020 07:17:04: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:17:04: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:17:04: #1 total tags in treatment: 15062020 INFO @ Tue, 14 Jul 2020 07:17:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:17:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:17:05: #1 tags after filtering in treatment: 15062020 INFO @ Tue, 14 Jul 2020 07:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:17:05: #1 finished! INFO @ Tue, 14 Jul 2020 07:17:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:17:06: #2 number of paired peaks: 793 WARNING @ Tue, 14 Jul 2020 07:17:06: Fewer paired peaks (793) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 793 pairs to build model! INFO @ Tue, 14 Jul 2020 07:17:06: start model_add_line... INFO @ Tue, 14 Jul 2020 07:17:06: start X-correlation... INFO @ Tue, 14 Jul 2020 07:17:06: end of X-cor INFO @ Tue, 14 Jul 2020 07:17:06: #2 finished! INFO @ Tue, 14 Jul 2020 07:17:06: #2 predicted fragment length is 66 bps INFO @ Tue, 14 Jul 2020 07:17:06: #2 alternative fragment length(s) may be 4,66 bps INFO @ Tue, 14 Jul 2020 07:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.20_model.r WARNING @ Tue, 14 Jul 2020 07:17:06: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:17:06: #2 You may need to consider one of the other alternative d(s): 4,66 WARNING @ Tue, 14 Jul 2020 07:17:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:17:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.10_summits.bed INFO @ Tue, 14 Jul 2020 07:17:17: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2433 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532033/SRX1532033.20_summits.bed INFO @ Tue, 14 Jul 2020 07:17:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1252 records, 4 fields): 13 millis CompletedMACS2peakCalling