Job ID = 6527858 SRX = SRX287889 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:33:56 prefetch.2.10.7: 1) Downloading 'SRR870078'... 2020-06-29T13:33:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:38:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:38:15 prefetch.2.10.7: 1) 'SRR870078' was downloaded successfully Read 22382823 spots for SRR870078/SRR870078.sra Written 22382823 spots for SRR870078/SRR870078.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: 00:07:57 22382823 reads; of these: 22382823 (100.00%) were unpaired; of these: 1147746 (5.13%) aligned 0 times 14422488 (64.44%) aligned exactly 1 time 6812589 (30.44%) aligned >1 times 94.87% overall alignment rate Time searching: 00:07:57 Overall time: 00:07:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4905327 / 21235077 = 0.2310 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 @ Mon, 29 Jun 2020 22:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.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 @ Mon, 29 Jun 2020 22:57:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:52: 1000000 INFO @ Mon, 29 Jun 2020 22:57:58: 2000000 INFO @ Mon, 29 Jun 2020 22:58:04: 3000000 INFO @ Mon, 29 Jun 2020 22:58:09: 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 @ Mon, 29 Jun 2020 22:58:15: 5000000 INFO @ Mon, 29 Jun 2020 22:58:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.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 @ Mon, 29 Jun 2020 22:58:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:22: 6000000 INFO @ Mon, 29 Jun 2020 22:58:23: 1000000 INFO @ Mon, 29 Jun 2020 22:58:28: 7000000 INFO @ Mon, 29 Jun 2020 22:58:29: 2000000 INFO @ Mon, 29 Jun 2020 22:58:35: 8000000 INFO @ Mon, 29 Jun 2020 22:58:36: 3000000 INFO @ Mon, 29 Jun 2020 22:58:41: 9000000 INFO @ Mon, 29 Jun 2020 22:58:43: 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 @ Mon, 29 Jun 2020 22:58:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.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 @ Mon, 29 Jun 2020 22:58:47: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:47: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:48: 10000000 INFO @ Mon, 29 Jun 2020 22:58:49: 5000000 INFO @ Mon, 29 Jun 2020 22:58:54: 1000000 INFO @ Mon, 29 Jun 2020 22:58:55: 11000000 INFO @ Mon, 29 Jun 2020 22:58:57: 6000000 INFO @ Mon, 29 Jun 2020 22:59:02: 2000000 INFO @ Mon, 29 Jun 2020 22:59:03: 12000000 INFO @ Mon, 29 Jun 2020 22:59:04: 7000000 INFO @ Mon, 29 Jun 2020 22:59:10: 3000000 INFO @ Mon, 29 Jun 2020 22:59:10: 13000000 INFO @ Mon, 29 Jun 2020 22:59:11: 8000000 INFO @ Mon, 29 Jun 2020 22:59:17: 4000000 INFO @ Mon, 29 Jun 2020 22:59:17: 14000000 INFO @ Mon, 29 Jun 2020 22:59:19: 9000000 INFO @ Mon, 29 Jun 2020 22:59:25: 15000000 INFO @ Mon, 29 Jun 2020 22:59:25: 5000000 INFO @ Mon, 29 Jun 2020 22:59:27: 10000000 INFO @ Mon, 29 Jun 2020 22:59:33: 16000000 INFO @ Mon, 29 Jun 2020 22:59:33: 6000000 INFO @ Mon, 29 Jun 2020 22:59:34: 11000000 INFO @ Mon, 29 Jun 2020 22:59:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:59:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:59:35: #1 total tags in treatment: 16329750 INFO @ Mon, 29 Jun 2020 22:59:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:59:35: #1 tags after filtering in treatment: 16329750 INFO @ Mon, 29 Jun 2020 22:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:35: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:37: #2 number of paired peaks: 199 WARNING @ Mon, 29 Jun 2020 22:59:37: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:37: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:37: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:37: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:37: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:37: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 22:59:37: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 22:59:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.05_model.r WARNING @ Mon, 29 Jun 2020 22:59:37: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:59:37: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 22:59:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:59:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:41: 7000000 INFO @ Mon, 29 Jun 2020 22:59:42: 12000000 INFO @ Mon, 29 Jun 2020 22:59:48: 8000000 INFO @ Mon, 29 Jun 2020 22:59:49: 13000000 INFO @ Mon, 29 Jun 2020 22:59:56: 9000000 INFO @ Mon, 29 Jun 2020 22:59:57: 14000000 INFO @ Mon, 29 Jun 2020 23:00:03: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:00:04: 15000000 INFO @ Mon, 29 Jun 2020 23:00:09: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:11: 11000000 INFO @ Mon, 29 Jun 2020 23:00:12: 16000000 INFO @ Mon, 29 Jun 2020 23:00:15: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:00:15: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:00:15: #1 total tags in treatment: 16329750 INFO @ Mon, 29 Jun 2020 23:00:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:00:15: #1 tags after filtering in treatment: 16329750 INFO @ Mon, 29 Jun 2020 23:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:15: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:00:16: #2 number of paired peaks: 199 WARNING @ Mon, 29 Jun 2020 23:00:16: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Mon, 29 Jun 2020 23:00:16: start model_add_line... INFO @ Mon, 29 Jun 2020 23:00:16: start X-correlation... INFO @ Mon, 29 Jun 2020 23:00:16: end of X-cor INFO @ Mon, 29 Jun 2020 23:00:16: #2 finished! INFO @ Mon, 29 Jun 2020 23:00:16: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:00:16: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.10_model.r WARNING @ Mon, 29 Jun 2020 23:00:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:00:16: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:00:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:00:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:00:18: 12000000 INFO @ Mon, 29 Jun 2020 23:00:25: 13000000 INFO @ Mon, 29 Jun 2020 23:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:00:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.05_summits.bed INFO @ Mon, 29 Jun 2020 23:00:26: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2202 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:00:33: 14000000 INFO @ Mon, 29 Jun 2020 23:00:40: 15000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:00:46: 16000000 INFO @ Mon, 29 Jun 2020 23:00:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:00:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:00:49: #1 total tags in treatment: 16329750 INFO @ Mon, 29 Jun 2020 23:00:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:00:49: #1 tags after filtering in treatment: 16329750 INFO @ Mon, 29 Jun 2020 23:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:49: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:00:50: #2 number of paired peaks: 199 WARNING @ Mon, 29 Jun 2020 23:00:50: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Mon, 29 Jun 2020 23:00:50: start model_add_line... INFO @ Mon, 29 Jun 2020 23:00:50: start X-correlation... INFO @ Mon, 29 Jun 2020 23:00:50: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:50: end of X-cor INFO @ Mon, 29 Jun 2020 23:00:50: #2 finished! INFO @ Mon, 29 Jun 2020 23:00:50: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:00:50: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.20_model.r WARNING @ Mon, 29 Jun 2020 23:00:50: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:00:50: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:00:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:00:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.10_summits.bed INFO @ Mon, 29 Jun 2020 23:01:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1817 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:01:22: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287889/SRX287889.20_summits.bed INFO @ Mon, 29 Jun 2020 23:01:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1291 records, 4 fields): 3 millis CompletedMACS2peakCalling