Job ID = 6453217 SRX = SRX1091591 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:18:02 prefetch.2.10.7: 1) Downloading 'SRR2096475'... 2020-06-21T08:18:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:20:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:20:48 prefetch.2.10.7: 'SRR2096475' is valid 2020-06-21T08:20:48 prefetch.2.10.7: 1) 'SRR2096475' was downloaded successfully 2020-06-21T08:20:48 prefetch.2.10.7: 'SRR2096475' has 0 unresolved dependencies Read 4660093 spots for SRR2096475/SRR2096475.sra Written 4660093 spots for SRR2096475/SRR2096475.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: 00:03:34 4660093 reads; of these: 4660093 (100.00%) were unpaired; of these: 302070 (6.48%) aligned 0 times 3723645 (79.90%) aligned exactly 1 time 634378 (13.61%) aligned >1 times 93.52% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 227032 / 4358023 = 0.0521 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 17:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.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 17:27:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:09: 1000000 INFO @ Sun, 21 Jun 2020 17:28:19: 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 17:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.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 17:28:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:29: 3000000 INFO @ Sun, 21 Jun 2020 17:28:40: 1000000 INFO @ Sun, 21 Jun 2020 17:28:40: 4000000 INFO @ Sun, 21 Jun 2020 17:28:42: #1 tag size is determined as 147 bps INFO @ Sun, 21 Jun 2020 17:28:42: #1 tag size = 147 INFO @ Sun, 21 Jun 2020 17:28:42: #1 total tags in treatment: 4130991 INFO @ Sun, 21 Jun 2020 17:28:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:42: #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 17:28:42: #1 tags after filtering in treatment: 4130706 INFO @ Sun, 21 Jun 2020 17:28:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:42: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:43: #2 number of paired peaks: 769 WARNING @ Sun, 21 Jun 2020 17:28:43: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Sun, 21 Jun 2020 17:28:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:43: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 17:28:43: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 17:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.05_model.r WARNING @ Sun, 21 Jun 2020 17:28:43: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:28:43: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sun, 21 Jun 2020 17:28:43: #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 17:28:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:50: 2000000 INFO @ Sun, 21 Jun 2020 17:28:54: #3 Call peaks for each chromosome... 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 17:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.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 17:28:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.05_summits.bed INFO @ Sun, 21 Jun 2020 17:29:00: Done! pass1 - making usageList (196 chroms): 1 millis pass2 - checking and writing primary data (3052 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:29:00: 3000000 INFO @ Sun, 21 Jun 2020 17:29:10: 1000000 INFO @ Sun, 21 Jun 2020 17:29:12: 4000000 INFO @ Sun, 21 Jun 2020 17:29:13: #1 tag size is determined as 147 bps INFO @ Sun, 21 Jun 2020 17:29:13: #1 tag size = 147 INFO @ Sun, 21 Jun 2020 17:29:13: #1 total tags in treatment: 4130991 INFO @ Sun, 21 Jun 2020 17:29:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:13: #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 17:29:14: #1 tags after filtering in treatment: 4130706 INFO @ Sun, 21 Jun 2020 17:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:14: #2 number of paired peaks: 769 WARNING @ Sun, 21 Jun 2020 17:29:14: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Sun, 21 Jun 2020 17:29:14: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:14: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:14: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:14: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:14: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 17:29:14: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 17:29:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.10_model.r WARNING @ Sun, 21 Jun 2020 17:29:14: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:29:14: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sun, 21 Jun 2020 17:29:14: #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 17:29:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:21: 2000000 INFO @ Sun, 21 Jun 2020 17:29:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.10_summits.bed INFO @ Sun, 21 Jun 2020 17:29:31: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (774 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:29:31: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:41: 4000000 INFO @ Sun, 21 Jun 2020 17:29:43: #1 tag size is determined as 147 bps INFO @ Sun, 21 Jun 2020 17:29:43: #1 tag size = 147 INFO @ Sun, 21 Jun 2020 17:29:43: #1 total tags in treatment: 4130991 INFO @ Sun, 21 Jun 2020 17:29:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:43: #1 tags after filtering in treatment: 4130706 INFO @ Sun, 21 Jun 2020 17:29:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:43: #2 number of paired peaks: 769 WARNING @ Sun, 21 Jun 2020 17:29:43: Fewer paired peaks (769) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 769 pairs to build model! INFO @ Sun, 21 Jun 2020 17:29:43: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:43: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:43: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:43: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:43: #2 predicted fragment length is 163 bps INFO @ Sun, 21 Jun 2020 17:29:43: #2 alternative fragment length(s) may be 163 bps INFO @ Sun, 21 Jun 2020 17:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.20_model.r WARNING @ Sun, 21 Jun 2020 17:29:43: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:29:43: #2 You may need to consider one of the other alternative d(s): 163 WARNING @ Sun, 21 Jun 2020 17:29:43: #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 17:29:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091591/SRX1091591.20_summits.bed INFO @ Sun, 21 Jun 2020 17:29:59: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (217 records, 4 fields): 3 millis CompletedMACS2peakCalling