Job ID = 6455492 SRX = SRX287829 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:40 prefetch.2.10.7: 1) Downloading 'SRR870018'... 2020-06-21T10:02:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:05:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:05:03 prefetch.2.10.7: 'SRR870018' is valid 2020-06-21T10:05:03 prefetch.2.10.7: 1) 'SRR870018' was downloaded successfully Read 13809114 spots for SRR870018/SRR870018.sra Written 13809114 spots for SRR870018/SRR870018.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:17 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756604 (5.48%) aligned 0 times 9039919 (65.46%) aligned exactly 1 time 4012591 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 2217228 / 13052510 = 0.1699 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 19:13:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.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 19:13:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:50: 1000000 INFO @ Sun, 21 Jun 2020 19:13:56: 2000000 INFO @ Sun, 21 Jun 2020 19:14:02: 3000000 INFO @ Sun, 21 Jun 2020 19:14:08: 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 19:14:14: 5000000 INFO @ Sun, 21 Jun 2020 19:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.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 19:14:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:20: 6000000 INFO @ Sun, 21 Jun 2020 19:14:21: 1000000 INFO @ Sun, 21 Jun 2020 19:14:26: 7000000 INFO @ Sun, 21 Jun 2020 19:14:27: 2000000 INFO @ Sun, 21 Jun 2020 19:14:32: 8000000 INFO @ Sun, 21 Jun 2020 19:14:33: 3000000 INFO @ Sun, 21 Jun 2020 19:14:39: 9000000 INFO @ Sun, 21 Jun 2020 19:14:40: 4000000 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 19:14:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.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 19:14:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:46: 10000000 INFO @ Sun, 21 Jun 2020 19:14:47: 5000000 INFO @ Sun, 21 Jun 2020 19:14:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:52: #1 total tags in treatment: 10835282 INFO @ Sun, 21 Jun 2020 19:14:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:52: #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 19:14:52: 1000000 INFO @ Sun, 21 Jun 2020 19:14:52: #1 tags after filtering in treatment: 10835282 INFO @ Sun, 21 Jun 2020 19:14:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:53: #2 number of paired peaks: 713 WARNING @ Sun, 21 Jun 2020 19:14:53: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:53: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:14:53: #2 alternative fragment length(s) may be 4,43,556 bps INFO @ Sun, 21 Jun 2020 19:14:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.05_model.r WARNING @ Sun, 21 Jun 2020 19:14:53: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:53: #2 You may need to consider one of the other alternative d(s): 4,43,556 WARNING @ Sun, 21 Jun 2020 19:14:53: #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 19:14:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:14:53: 6000000 INFO @ Sun, 21 Jun 2020 19:15:00: 2000000 INFO @ Sun, 21 Jun 2020 19:15:00: 7000000 INFO @ Sun, 21 Jun 2020 19:15:07: 3000000 INFO @ Sun, 21 Jun 2020 19:15:07: 8000000 INFO @ Sun, 21 Jun 2020 19:15:15: 4000000 INFO @ Sun, 21 Jun 2020 19:15:15: 9000000 INFO @ Sun, 21 Jun 2020 19:15:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:21: 10000000 INFO @ Sun, 21 Jun 2020 19:15:22: 5000000 INFO @ Sun, 21 Jun 2020 19:15:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.05_summits.bed INFO @ Sun, 21 Jun 2020 19:15:27: Done! pass1 - making usageList (583 chroms): 2 millis pass2 - checking and writing primary data (2242 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:15:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:27: #1 total tags in treatment: 10835282 INFO @ Sun, 21 Jun 2020 19:15:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:27: #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 19:15:28: #1 tags after filtering in treatment: 10835282 INFO @ Sun, 21 Jun 2020 19:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:29: #2 number of paired peaks: 713 WARNING @ Sun, 21 Jun 2020 19:15:29: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:29: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:15:29: #2 alternative fragment length(s) may be 4,43,556 bps INFO @ Sun, 21 Jun 2020 19:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.10_model.r WARNING @ Sun, 21 Jun 2020 19:15:29: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:29: #2 You may need to consider one of the other alternative d(s): 4,43,556 WARNING @ Sun, 21 Jun 2020 19:15:29: #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 19:15:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:29: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:15:36: 7000000 INFO @ Sun, 21 Jun 2020 19:15:43: 8000000 INFO @ Sun, 21 Jun 2020 19:15:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:50: 9000000 INFO @ Sun, 21 Jun 2020 19:15:57: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.10_summits.bed INFO @ Sun, 21 Jun 2020 19:16:01: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (1834 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:03: #1 total tags in treatment: 10835282 INFO @ Sun, 21 Jun 2020 19:16:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:03: #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 19:16:04: #1 tags after filtering in treatment: 10835282 INFO @ Sun, 21 Jun 2020 19:16:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:04: #2 number of paired peaks: 713 WARNING @ Sun, 21 Jun 2020 19:16:04: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:04: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:16:04: #2 alternative fragment length(s) may be 4,43,556 bps INFO @ Sun, 21 Jun 2020 19:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.20_model.r WARNING @ Sun, 21 Jun 2020 19:16:04: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:04: #2 You may need to consider one of the other alternative d(s): 4,43,556 WARNING @ Sun, 21 Jun 2020 19:16:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:16:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287829/SRX287829.20_summits.bed INFO @ Sun, 21 Jun 2020 19:16:37: Done! pass1 - making usageList (314 chroms): 1 millis pass2 - checking and writing primary data (653 records, 4 fields): 11 millis CompletedMACS2peakCalling