Job ID = 6455047 SRX = SRX2642394 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:54:10 prefetch.2.10.7: 1) Downloading 'SRR5345734'... 2020-06-21T09:54:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:54:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:54:44 prefetch.2.10.7: 'SRR5345734' is valid 2020-06-21T09:54:44 prefetch.2.10.7: 1) 'SRR5345734' was downloaded successfully 2020-06-21T09:54:44 prefetch.2.10.7: 'SRR5345734' has 0 unresolved dependencies Read 2360750 spots for SRR5345734/SRR5345734.sra Written 2360750 spots for SRR5345734/SRR5345734.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: 00:01:15 2360750 reads; of these: 2360750 (100.00%) were unpaired; of these: 174532 (7.39%) aligned 0 times 1635424 (69.28%) aligned exactly 1 time 550794 (23.33%) aligned >1 times 92.61% overall alignment rate Time searching: 00:01:15 Overall time: 00:01:15 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_rmdupse_core] 39313 / 2186218 = 0.0180 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 18:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.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 18:57:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:57:35: 1000000 INFO @ Sun, 21 Jun 2020 18:57:45: 2000000 INFO @ Sun, 21 Jun 2020 18:57:46: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:57:46: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:57:46: #1 total tags in treatment: 2146905 INFO @ Sun, 21 Jun 2020 18:57:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:46: #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 18:57:46: #1 tags after filtering in treatment: 2146828 INFO @ Sun, 21 Jun 2020 18:57:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:46: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:47: #2 number of paired peaks: 513 WARNING @ Sun, 21 Jun 2020 18:57:47: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sun, 21 Jun 2020 18:57:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:47: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:57:47: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 18:57:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.05_model.r WARNING @ Sun, 21 Jun 2020 18:57:47: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:57:47: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 18:57:47: #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 18:57:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:57:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:54: Done! pass1 - making usageList (222 chroms): 0 millis pass2 - checking and writing primary data (427 records, 4 fields): 8 millis CompletedMACS2peakCalling 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 18:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.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 18:57:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:57:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:05: 1000000 INFO @ Sun, 21 Jun 2020 18:58:14: 2000000 INFO @ Sun, 21 Jun 2020 18:58:16: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:58:16: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:58:16: #1 total tags in treatment: 2146905 INFO @ Sun, 21 Jun 2020 18:58:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:16: #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 18:58:16: #1 tags after filtering in treatment: 2146828 INFO @ Sun, 21 Jun 2020 18:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:16: #2 number of paired peaks: 513 WARNING @ Sun, 21 Jun 2020 18:58:16: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:16: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:58:16: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 18:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.10_model.r WARNING @ Sun, 21 Jun 2020 18:58:16: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:16: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 18:58:16: #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 18:58:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.10_summits.bed INFO @ Sun, 21 Jun 2020 18:58:24: Done! pass1 - making usageList (143 chroms): 0 millis pass2 - checking and writing primary data (242 records, 4 fields): 6 millis BedGraph に変換中... CompletedMACS2peakCalling 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 18:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.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 18:58:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:58:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:58:35: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:58:45: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:58:46: #1 tag size is determined as 101 bps INFO @ Sun, 21 Jun 2020 18:58:46: #1 tag size = 101 INFO @ Sun, 21 Jun 2020 18:58:46: #1 total tags in treatment: 2146905 INFO @ Sun, 21 Jun 2020 18:58:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:58:46: #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 18:58:47: #1 tags after filtering in treatment: 2146828 INFO @ Sun, 21 Jun 2020 18:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:58:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:58:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:58:47: #2 number of paired peaks: 513 WARNING @ Sun, 21 Jun 2020 18:58:47: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Sun, 21 Jun 2020 18:58:47: start model_add_line... INFO @ Sun, 21 Jun 2020 18:58:47: start X-correlation... INFO @ Sun, 21 Jun 2020 18:58:47: end of X-cor INFO @ Sun, 21 Jun 2020 18:58:47: #2 finished! INFO @ Sun, 21 Jun 2020 18:58:47: #2 predicted fragment length is 106 bps INFO @ Sun, 21 Jun 2020 18:58:47: #2 alternative fragment length(s) may be 106 bps INFO @ Sun, 21 Jun 2020 18:58:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.20_model.r WARNING @ Sun, 21 Jun 2020 18:58:47: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:58:47: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sun, 21 Jun 2020 18:58:47: #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 18:58:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:58:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:58:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2642394/SRX2642394.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:55: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling