Job ID = 6455336 SRX = SRX287705 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:56:10 prefetch.2.10.7: 1) Downloading 'SRR869893'... 2020-06-21T09:56:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:58:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:58:53 prefetch.2.10.7: 1) 'SRR869893' was downloaded successfully Read 17570684 spots for SRR869893/SRR869893.sra Written 17570684 spots for SRR869893/SRR869893.sra 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: 00:06:06 17570684 reads; of these: 17570684 (100.00%) were unpaired; of these: 1164843 (6.63%) aligned 0 times 11092358 (63.13%) aligned exactly 1 time 5313483 (30.24%) aligned >1 times 93.37% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 3298251 / 16405841 = 0.2010 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 @ Sun, 21 Jun 2020 19:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.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 @ Sun, 21 Jun 2020 19:11:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:11:37: 1000000 INFO @ Sun, 21 Jun 2020 19:11:46: 2000000 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 @ Sun, 21 Jun 2020 19:11:55: 3000000 INFO @ Sun, 21 Jun 2020 19:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.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 @ Sun, 21 Jun 2020 19:11:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:11:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:05: 4000000 INFO @ Sun, 21 Jun 2020 19:12:06: 1000000 INFO @ Sun, 21 Jun 2020 19:12:13: 5000000 INFO @ Sun, 21 Jun 2020 19:12:15: 2000000 INFO @ Sun, 21 Jun 2020 19:12:22: 6000000 INFO @ Sun, 21 Jun 2020 19:12:24: 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 @ Sun, 21 Jun 2020 19:12:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.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 @ Sun, 21 Jun 2020 19:12:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:30: 7000000 INFO @ Sun, 21 Jun 2020 19:12:33: 4000000 INFO @ Sun, 21 Jun 2020 19:12:36: 1000000 INFO @ Sun, 21 Jun 2020 19:12:38: 8000000 INFO @ Sun, 21 Jun 2020 19:12:41: 5000000 INFO @ Sun, 21 Jun 2020 19:12:44: 2000000 INFO @ Sun, 21 Jun 2020 19:12:46: 9000000 INFO @ Sun, 21 Jun 2020 19:12:49: 6000000 INFO @ Sun, 21 Jun 2020 19:12:52: 3000000 INFO @ Sun, 21 Jun 2020 19:12:54: 10000000 INFO @ Sun, 21 Jun 2020 19:12:57: 7000000 INFO @ Sun, 21 Jun 2020 19:13:00: 4000000 INFO @ Sun, 21 Jun 2020 19:13:03: 11000000 INFO @ Sun, 21 Jun 2020 19:13:05: 8000000 INFO @ Sun, 21 Jun 2020 19:13:09: 5000000 INFO @ Sun, 21 Jun 2020 19:13:10: 12000000 INFO @ Sun, 21 Jun 2020 19:13:13: 9000000 INFO @ Sun, 21 Jun 2020 19:13:16: 6000000 INFO @ Sun, 21 Jun 2020 19:13:18: 13000000 INFO @ Sun, 21 Jun 2020 19:13:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:19: #1 total tags in treatment: 13107590 INFO @ Sun, 21 Jun 2020 19:13:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:13:20: #1 tags after filtering in treatment: 13107590 INFO @ Sun, 21 Jun 2020 19:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:20: 10000000 INFO @ Sun, 21 Jun 2020 19:13:21: #2 number of paired peaks: 571 WARNING @ Sun, 21 Jun 2020 19:13:21: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:21: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:13:21: #2 alternative fragment length(s) may be 3,41,543 bps INFO @ Sun, 21 Jun 2020 19:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.05_model.r WARNING @ Sun, 21 Jun 2020 19:13:21: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:21: #2 You may need to consider one of the other alternative d(s): 3,41,543 WARNING @ Sun, 21 Jun 2020 19:13:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:13:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:24: 7000000 INFO @ Sun, 21 Jun 2020 19:13:29: 11000000 INFO @ Sun, 21 Jun 2020 19:13:31: 8000000 INFO @ Sun, 21 Jun 2020 19:13:36: 12000000 INFO @ Sun, 21 Jun 2020 19:13:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:13:43: 13000000 INFO @ Sun, 21 Jun 2020 19:13:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:44: #1 total tags in treatment: 13107590 INFO @ Sun, 21 Jun 2020 19:13:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:13:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:45: #1 tags after filtering in treatment: 13107590 INFO @ Sun, 21 Jun 2020 19:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:45: 10000000 INFO @ Sun, 21 Jun 2020 19:13:46: #2 number of paired peaks: 571 WARNING @ Sun, 21 Jun 2020 19:13:46: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:46: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:13:46: #2 alternative fragment length(s) may be 3,41,543 bps INFO @ Sun, 21 Jun 2020 19:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.10_model.r WARNING @ Sun, 21 Jun 2020 19:13:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:46: #2 You may need to consider one of the other alternative d(s): 3,41,543 WARNING @ Sun, 21 Jun 2020 19:13:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:13:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:52: 11000000 INFO @ Sun, 21 Jun 2020 19:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:57: Done! pass1 - making usageList (593 chroms): 1 millis pass2 - checking and writing primary data (2397 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:58: 12000000 INFO @ Sun, 21 Jun 2020 19:14:04: 13000000 INFO @ Sun, 21 Jun 2020 19:14:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:05: #1 total tags in treatment: 13107590 INFO @ Sun, 21 Jun 2020 19:14:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:14:06: #1 tags after filtering in treatment: 13107590 INFO @ Sun, 21 Jun 2020 19:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:07: #2 number of paired peaks: 571 WARNING @ Sun, 21 Jun 2020 19:14:07: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:07: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:14:07: #2 alternative fragment length(s) may be 3,41,543 bps INFO @ Sun, 21 Jun 2020 19:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.20_model.r WARNING @ Sun, 21 Jun 2020 19:14:07: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:07: #2 You may need to consider one of the other alternative d(s): 3,41,543 WARNING @ Sun, 21 Jun 2020 19:14:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:14:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:14:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:21: Done! pass1 - making usageList (496 chroms): 2 millis pass2 - checking and writing primary data (1791 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287705/SRX287705.20_summits.bed INFO @ Sun, 21 Jun 2020 19:14:43: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (597 records, 4 fields): 17 millis CompletedMACS2peakCalling