Job ID = 6458964 SRX = SRX5827832 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:45:11 prefetch.2.10.7: 1) Downloading 'SRR9051583'... 2020-06-21T12:45:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:47:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:47:54 prefetch.2.10.7: 'SRR9051583' is valid 2020-06-21T12:47:54 prefetch.2.10.7: 1) 'SRR9051583' was downloaded successfully 2020-06-21T12:47:54 prefetch.2.10.7: 'SRR9051583' has 0 unresolved dependencies Read 21584059 spots for SRR9051583/SRR9051583.sra Written 21584059 spots for SRR9051583/SRR9051583.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: 00:04:46 21584059 reads; of these: 21584059 (100.00%) were unpaired; of these: 5263242 (24.38%) aligned 0 times 13498331 (62.54%) aligned exactly 1 time 2822486 (13.08%) aligned >1 times 75.62% overall alignment rate Time searching: 00:04:46 Overall time: 00:04:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4325923 / 16320817 = 0.2651 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 21:58:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.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 21:58:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:58:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:58:49: 1000000 INFO @ Sun, 21 Jun 2020 21:58:56: 2000000 INFO @ Sun, 21 Jun 2020 21:59:02: 3000000 INFO @ Sun, 21 Jun 2020 21:59:08: 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 @ Sun, 21 Jun 2020 21:59:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.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 21:59:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:15: 5000000 INFO @ Sun, 21 Jun 2020 21:59:20: 1000000 INFO @ Sun, 21 Jun 2020 21:59:22: 6000000 INFO @ Sun, 21 Jun 2020 21:59:27: 2000000 INFO @ Sun, 21 Jun 2020 21:59:29: 7000000 INFO @ Sun, 21 Jun 2020 21:59:34: 3000000 INFO @ Sun, 21 Jun 2020 21:59:36: 8000000 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 21:59:41: 4000000 INFO @ Sun, 21 Jun 2020 21:59:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.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 21:59:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:43: 9000000 INFO @ Sun, 21 Jun 2020 21:59:49: 5000000 INFO @ Sun, 21 Jun 2020 21:59:50: 1000000 INFO @ Sun, 21 Jun 2020 21:59:51: 10000000 INFO @ Sun, 21 Jun 2020 21:59:56: 6000000 INFO @ Sun, 21 Jun 2020 21:59:57: 2000000 INFO @ Sun, 21 Jun 2020 21:59:58: 11000000 INFO @ Sun, 21 Jun 2020 22:00:03: 7000000 INFO @ Sun, 21 Jun 2020 22:00:04: 3000000 INFO @ Sun, 21 Jun 2020 22:00:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:00:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:00:05: #1 total tags in treatment: 11994894 INFO @ Sun, 21 Jun 2020 22:00:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:05: #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 22:00:06: #1 tags after filtering in treatment: 11994893 INFO @ Sun, 21 Jun 2020 22:00:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:06: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:07: #2 number of paired peaks: 331 WARNING @ Sun, 21 Jun 2020 22:00:07: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:07: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 22:00:07: #2 alternative fragment length(s) may be 67,94 bps INFO @ Sun, 21 Jun 2020 22:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.05_model.r WARNING @ Sun, 21 Jun 2020 22:00:07: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:07: #2 You may need to consider one of the other alternative d(s): 67,94 WARNING @ Sun, 21 Jun 2020 22:00:07: #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 22:00:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:10: 8000000 INFO @ Sun, 21 Jun 2020 22:00:11: 4000000 INFO @ Sun, 21 Jun 2020 22:00:17: 9000000 INFO @ Sun, 21 Jun 2020 22:00:17: 5000000 INFO @ Sun, 21 Jun 2020 22:00:24: 10000000 INFO @ Sun, 21 Jun 2020 22:00:24: 6000000 INFO @ Sun, 21 Jun 2020 22:00:30: 11000000 INFO @ Sun, 21 Jun 2020 22:00:30: 7000000 INFO @ Sun, 21 Jun 2020 22:00:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:00:37: 8000000 INFO @ Sun, 21 Jun 2020 22:00:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:00:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:00:37: #1 total tags in treatment: 11994894 INFO @ Sun, 21 Jun 2020 22:00:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:37: #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 22:00:38: #1 tags after filtering in treatment: 11994893 INFO @ Sun, 21 Jun 2020 22:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:38: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:38: #2 number of paired peaks: 331 WARNING @ Sun, 21 Jun 2020 22:00:38: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:39: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:39: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:39: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:39: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 22:00:39: #2 alternative fragment length(s) may be 67,94 bps INFO @ Sun, 21 Jun 2020 22:00:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.10_model.r WARNING @ Sun, 21 Jun 2020 22:00:39: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:39: #2 You may need to consider one of the other alternative d(s): 67,94 WARNING @ Sun, 21 Jun 2020 22:00:39: #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 22:00:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:43: Done! INFO @ Sun, 21 Jun 2020 22:00:43: 9000000 pass1 - making usageList (449 chroms): 1 millis pass2 - checking and writing primary data (2364 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:49: 10000000 INFO @ Sun, 21 Jun 2020 22:00:55: 11000000 INFO @ Sun, 21 Jun 2020 22:01:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:01:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:01:01: #1 total tags in treatment: 11994894 INFO @ Sun, 21 Jun 2020 22:01:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:01: #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 22:01:01: #1 tags after filtering in treatment: 11994893 INFO @ Sun, 21 Jun 2020 22:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:02: #2 number of paired peaks: 331 WARNING @ Sun, 21 Jun 2020 22:01:02: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Sun, 21 Jun 2020 22:01:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:02: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 22:01:02: #2 alternative fragment length(s) may be 67,94 bps INFO @ Sun, 21 Jun 2020 22:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.20_model.r WARNING @ Sun, 21 Jun 2020 22:01:02: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:02: #2 You may need to consider one of the other alternative d(s): 67,94 WARNING @ Sun, 21 Jun 2020 22:01:02: #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 22:01:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:01:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.10_summits.bed INFO @ Sun, 21 Jun 2020 22:01:14: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (1294 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5827832/SRX5827832.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:37: Done! pass1 - making usageList (170 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 6 millis CompletedMACS2peakCalling