Job ID = 6529522 SRX = SRX287915 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: 00:04:21 16042597 reads; of these: 16042597 (100.00%) were unpaired; of these: 892074 (5.56%) aligned 0 times 11800573 (73.56%) aligned exactly 1 time 3349950 (20.88%) aligned >1 times 94.44% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 1345655 / 15150523 = 0.0888 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 02:25:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.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 02:25:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:50: 1000000 INFO @ Tue, 30 Jun 2020 02:25:56: 2000000 INFO @ Tue, 30 Jun 2020 02:26:01: 3000000 INFO @ Tue, 30 Jun 2020 02:26:07: 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 02:26:13: 5000000 INFO @ Tue, 30 Jun 2020 02:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.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 02:26:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:26:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:26:19: 6000000 INFO @ Tue, 30 Jun 2020 02:26:20: 1000000 INFO @ Tue, 30 Jun 2020 02:26:24: 7000000 INFO @ Tue, 30 Jun 2020 02:26:25: 2000000 INFO @ Tue, 30 Jun 2020 02:26:30: 8000000 INFO @ Tue, 30 Jun 2020 02:26:31: 3000000 INFO @ Tue, 30 Jun 2020 02:26:36: 9000000 INFO @ Tue, 30 Jun 2020 02:26:37: 4000000 INFO @ Tue, 30 Jun 2020 02:26:41: 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 02:26:42: 5000000 INFO @ Tue, 30 Jun 2020 02:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.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 02:26:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:26:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:26:47: 11000000 INFO @ Tue, 30 Jun 2020 02:26:48: 6000000 INFO @ Tue, 30 Jun 2020 02:26:51: 1000000 INFO @ Tue, 30 Jun 2020 02:26:54: 12000000 INFO @ Tue, 30 Jun 2020 02:26:54: 7000000 INFO @ Tue, 30 Jun 2020 02:26:58: 2000000 INFO @ Tue, 30 Jun 2020 02:27:00: 13000000 INFO @ Tue, 30 Jun 2020 02:27:00: 8000000 INFO @ Tue, 30 Jun 2020 02:27:05: 3000000 INFO @ Tue, 30 Jun 2020 02:27:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:06: #1 total tags in treatment: 13804868 INFO @ Tue, 30 Jun 2020 02:27:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:06: #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 02:27:06: 9000000 INFO @ Tue, 30 Jun 2020 02:27:06: #1 tags after filtering in treatment: 13804862 INFO @ Tue, 30 Jun 2020 02:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:07: #2 number of paired peaks: 266 WARNING @ Tue, 30 Jun 2020 02:27:07: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:07: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:27:07: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 30 Jun 2020 02:27:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.05_model.r WARNING @ Tue, 30 Jun 2020 02:27:07: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:07: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 30 Jun 2020 02:27:07: #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 02:27:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:12: 10000000 INFO @ Tue, 30 Jun 2020 02:27:12: 4000000 INFO @ Tue, 30 Jun 2020 02:27:17: 11000000 INFO @ Tue, 30 Jun 2020 02:27:18: 5000000 INFO @ Tue, 30 Jun 2020 02:27:24: 12000000 INFO @ Tue, 30 Jun 2020 02:27:25: 6000000 INFO @ Tue, 30 Jun 2020 02:27:30: 13000000 INFO @ Tue, 30 Jun 2020 02:27:32: 7000000 INFO @ Tue, 30 Jun 2020 02:27:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:27:35: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:35: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:35: #1 total tags in treatment: 13804868 INFO @ Tue, 30 Jun 2020 02:27:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:35: #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 02:27:36: #1 tags after filtering in treatment: 13804862 INFO @ Tue, 30 Jun 2020 02:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:37: #2 number of paired peaks: 266 WARNING @ Tue, 30 Jun 2020 02:27:37: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:37: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:27:37: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 30 Jun 2020 02:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.10_model.r WARNING @ Tue, 30 Jun 2020 02:27:37: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:27:37: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 30 Jun 2020 02:27:37: #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 02:27:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:38: 8000000 INFO @ Tue, 30 Jun 2020 02:27:45: 9000000 INFO @ Tue, 30 Jun 2020 02:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.05_summits.bed INFO @ Tue, 30 Jun 2020 02:27:48: Done! pass1 - making usageList (382 chroms): 2 millis pass2 - checking and writing primary data (2250 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:51: 10000000 INFO @ Tue, 30 Jun 2020 02:27:56: 11000000 INFO @ Tue, 30 Jun 2020 02:28:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:28:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:28:09: 13000000 INFO @ Tue, 30 Jun 2020 02:28:14: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:14: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:14: #1 total tags in treatment: 13804868 INFO @ Tue, 30 Jun 2020 02:28:14: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:14: #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 02:28:14: #1 tags after filtering in treatment: 13804862 INFO @ Tue, 30 Jun 2020 02:28:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:15: #2 number of paired peaks: 266 WARNING @ Tue, 30 Jun 2020 02:28:15: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:15: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:15: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:16: #2 predicted fragment length is 81 bps INFO @ Tue, 30 Jun 2020 02:28:16: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 30 Jun 2020 02:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.20_model.r WARNING @ Tue, 30 Jun 2020 02:28:16: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:16: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 30 Jun 2020 02:28:16: #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 02:28:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.10_summits.bed INFO @ Tue, 30 Jun 2020 02:28:17: Done! pass1 - making usageList (290 chroms): 1 millis pass2 - checking and writing primary data (823 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:28:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287915/SRX287915.20_summits.bed INFO @ Tue, 30 Jun 2020 02:28:55: Done! pass1 - making usageList (149 chroms): 2 millis pass2 - checking and writing primary data (310 records, 4 fields): 9 millis CompletedMACS2peakCalling