Job ID = 6529588 SRX = SRX331376 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: 00:04:30 17353964 reads; of these: 17353964 (100.00%) were unpaired; of these: 1332609 (7.68%) aligned 0 times 12297135 (70.86%) aligned exactly 1 time 3724220 (21.46%) aligned >1 times 92.32% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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 8 files... [bam_rmdupse_core] 2762783 / 16021355 = 0.1724 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 02:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.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 02:23:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:11: 1000000 INFO @ Tue, 30 Jun 2020 02:23:16: 2000000 INFO @ Tue, 30 Jun 2020 02:23:21: 3000000 INFO @ Tue, 30 Jun 2020 02:23:26: 4000000 INFO @ Tue, 30 Jun 2020 02:23:31: 5000000 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 02:23:36: 6000000 INFO @ Tue, 30 Jun 2020 02:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.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 02:23:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:41: 7000000 INFO @ Tue, 30 Jun 2020 02:23:42: 1000000 INFO @ Tue, 30 Jun 2020 02:23:46: 8000000 INFO @ Tue, 30 Jun 2020 02:23:48: 2000000 INFO @ Tue, 30 Jun 2020 02:23:51: 9000000 INFO @ Tue, 30 Jun 2020 02:23:54: 3000000 INFO @ Tue, 30 Jun 2020 02:23:57: 10000000 INFO @ Tue, 30 Jun 2020 02:24:00: 4000000 INFO @ Tue, 30 Jun 2020 02:24:02: 11000000 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 02:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.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 02:24:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:06: 5000000 INFO @ Tue, 30 Jun 2020 02:24:07: 12000000 INFO @ Tue, 30 Jun 2020 02:24:11: 1000000 INFO @ Tue, 30 Jun 2020 02:24:12: 6000000 INFO @ Tue, 30 Jun 2020 02:24:13: 13000000 INFO @ Tue, 30 Jun 2020 02:24:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:14: #1 total tags in treatment: 13258572 INFO @ Tue, 30 Jun 2020 02:24:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:14: #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 02:24:15: #1 tags after filtering in treatment: 13258571 INFO @ Tue, 30 Jun 2020 02:24:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:15: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:16: #2 number of paired peaks: 625 WARNING @ Tue, 30 Jun 2020 02:24:16: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:16: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:24:16: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 02:24:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.05_model.r WARNING @ Tue, 30 Jun 2020 02:24:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:16: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 02:24:16: #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 02:24:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:17: 2000000 INFO @ Tue, 30 Jun 2020 02:24:18: 7000000 INFO @ Tue, 30 Jun 2020 02:24:22: 3000000 INFO @ Tue, 30 Jun 2020 02:24:24: 8000000 INFO @ Tue, 30 Jun 2020 02:24:27: 4000000 INFO @ Tue, 30 Jun 2020 02:24:30: 9000000 INFO @ Tue, 30 Jun 2020 02:24:32: 5000000 INFO @ Tue, 30 Jun 2020 02:24:36: 10000000 INFO @ Tue, 30 Jun 2020 02:24:38: 6000000 INFO @ Tue, 30 Jun 2020 02:24:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:24:43: 11000000 INFO @ Tue, 30 Jun 2020 02:24:43: 7000000 INFO @ Tue, 30 Jun 2020 02:24:48: 8000000 INFO @ Tue, 30 Jun 2020 02:24:48: 12000000 INFO @ Tue, 30 Jun 2020 02:24:53: 9000000 INFO @ Tue, 30 Jun 2020 02:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.05_summits.bed INFO @ Tue, 30 Jun 2020 02:24:54: Done! pass1 - making usageList (550 chroms): 2 millis pass2 - checking and writing primary data (2122 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:24:55: 13000000 INFO @ Tue, 30 Jun 2020 02:24:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:24:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:24:56: #1 total tags in treatment: 13258572 INFO @ Tue, 30 Jun 2020 02:24:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:56: #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 02:24:57: #1 tags after filtering in treatment: 13258571 INFO @ Tue, 30 Jun 2020 02:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:58: #2 number of paired peaks: 625 WARNING @ Tue, 30 Jun 2020 02:24:58: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:58: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:24:58: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 02:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.10_model.r WARNING @ Tue, 30 Jun 2020 02:24:58: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:58: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 02:24:58: #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 02:24:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:58: 10000000 INFO @ Tue, 30 Jun 2020 02:25:04: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:25:09: 12000000 INFO @ Tue, 30 Jun 2020 02:25:14: 13000000 INFO @ Tue, 30 Jun 2020 02:25:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:25:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:25:16: #1 total tags in treatment: 13258572 INFO @ Tue, 30 Jun 2020 02:25:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:16: #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 02:25:16: #1 tags after filtering in treatment: 13258571 INFO @ Tue, 30 Jun 2020 02:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:16: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:16: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:17: #2 number of paired peaks: 625 WARNING @ Tue, 30 Jun 2020 02:25:17: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:17: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:17: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:17: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:17: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:17: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 02:25:17: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 30 Jun 2020 02:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.20_model.r WARNING @ Tue, 30 Jun 2020 02:25:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:17: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 30 Jun 2020 02:25:17: #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 02:25:17: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:25:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.10_summits.bed INFO @ Tue, 30 Jun 2020 02:25:36: Done! pass1 - making usageList (456 chroms): 1 millis pass2 - checking and writing primary data (1723 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331376/SRX331376.20_summits.bed INFO @ Tue, 30 Jun 2020 02:25:54: Done! pass1 - making usageList (300 chroms): 1 millis pass2 - checking and writing primary data (636 records, 4 fields): 10 millis CompletedMACS2peakCalling