Job ID = 6458382 SRX = SRX507394 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:34 prefetch.2.10.7: 1) Downloading 'SRR1213181'... 2020-06-21T12:20:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:21:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:21:35 prefetch.2.10.7: 'SRR1213181' is valid 2020-06-21T12:21:35 prefetch.2.10.7: 1) 'SRR1213181' was downloaded successfully Read 7228130 spots for SRR1213181/SRR1213181.sra Written 7228130 spots for SRR1213181/SRR1213181.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: 00:01:29 7228130 reads; of these: 7228130 (100.00%) were unpaired; of these: 450994 (6.24%) aligned 0 times 5443572 (75.31%) aligned exactly 1 time 1333564 (18.45%) aligned >1 times 93.76% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 3346712 / 6777136 = 0.4938 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 21:25:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.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 21:25:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:21: 1000000 INFO @ Sun, 21 Jun 2020 21:25:26: 2000000 INFO @ Sun, 21 Jun 2020 21:25:32: 3000000 INFO @ Sun, 21 Jun 2020 21:25:34: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:34: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:34: #1 total tags in treatment: 3430424 INFO @ Sun, 21 Jun 2020 21:25:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:34: #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 21:25:35: #1 tags after filtering in treatment: 3430274 INFO @ Sun, 21 Jun 2020 21:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:35: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 21:25:35: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 21:25:35: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:35: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:35: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:35: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:35: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 21:25:35: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 21:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.05_model.r WARNING @ Sun, 21 Jun 2020 21:25:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:35: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 21:25:35: #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 21:25:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:43: #3 Call peaks for each chromosome... 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 21:25:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.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 21:25:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:47: Done! pass1 - making usageList (391 chroms): 1 millis pass2 - checking and writing primary data (1124 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:51: 1000000 INFO @ Sun, 21 Jun 2020 21:25:57: 2000000 INFO @ Sun, 21 Jun 2020 21:26:02: 3000000 INFO @ Sun, 21 Jun 2020 21:26:05: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:26:05: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:26:05: #1 total tags in treatment: 3430424 INFO @ Sun, 21 Jun 2020 21:26:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:05: #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 21:26:05: #1 tags after filtering in treatment: 3430274 INFO @ Sun, 21 Jun 2020 21:26:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:05: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:05: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 21:26:05: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 21:26:05: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:05: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:05: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:05: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:05: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 21:26:05: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 21:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.10_model.r WARNING @ Sun, 21 Jun 2020 21:26:05: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:05: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 21:26:05: #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 21:26:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:26:14: #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 21:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.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 21:26:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.10_summits.bed INFO @ Sun, 21 Jun 2020 21:26:18: Done! pass1 - making usageList (151 chroms): 1 millis pass2 - checking and writing primary data (356 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:26:21: 1000000 INFO @ Sun, 21 Jun 2020 21:26:27: 2000000 INFO @ Sun, 21 Jun 2020 21:26:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:26:35: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:26:35: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:26:35: #1 total tags in treatment: 3430424 INFO @ Sun, 21 Jun 2020 21:26:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:35: #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 21:26:35: #1 tags after filtering in treatment: 3430274 INFO @ Sun, 21 Jun 2020 21:26:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:35: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:36: #2 number of paired peaks: 919 WARNING @ Sun, 21 Jun 2020 21:26:36: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Sun, 21 Jun 2020 21:26:36: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:36: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:36: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:36: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:36: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 21:26:36: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 21:26:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.20_model.r WARNING @ Sun, 21 Jun 2020 21:26:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:36: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 21:26:36: #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 21:26:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX507394/SRX507394.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:48: Done! pass1 - making usageList (85 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 3 millis CompletedMACS2peakCalling