Job ID = 6454832 SRX = SRX2592428 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:45:25 prefetch.2.10.7: 1) Downloading 'SRR5289705'... 2020-06-21T09:45:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:47:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:47:04 prefetch.2.10.7: 'SRR5289705' is valid 2020-06-21T09:47:04 prefetch.2.10.7: 1) 'SRR5289705' was downloaded successfully Read 8403699 spots for SRR5289705/SRR5289705.sra Written 8403699 spots for SRR5289705/SRR5289705.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: 00:03:17 8403699 reads; of these: 8403699 (100.00%) were unpaired; of these: 937658 (11.16%) aligned 0 times 4847335 (57.68%) aligned exactly 1 time 2618706 (31.16%) aligned >1 times 88.84% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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] 2318892 / 7466041 = 0.3106 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 18:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.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 18:53:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:17: 1000000 INFO @ Sun, 21 Jun 2020 18:53:22: 2000000 INFO @ Sun, 21 Jun 2020 18:53:27: 3000000 INFO @ Sun, 21 Jun 2020 18:53:33: 4000000 INFO @ Sun, 21 Jun 2020 18:53:38: 5000000 INFO @ Sun, 21 Jun 2020 18:53:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:53:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:53:38: #1 total tags in treatment: 5147149 INFO @ Sun, 21 Jun 2020 18:53:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:53:38: #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 18:53:39: #1 tags after filtering in treatment: 5146983 INFO @ Sun, 21 Jun 2020 18:53:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:53:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:53:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:53:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:53:40: #2 number of paired peaks: 653 WARNING @ Sun, 21 Jun 2020 18:53:40: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Sun, 21 Jun 2020 18:53:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:53:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:53:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:53:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:53:40: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 18:53:40: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 18:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.05_model.r WARNING @ Sun, 21 Jun 2020 18:53:40: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:53:40: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 18:53:40: #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 18:53:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:53:40: #3 Pre-compute pvalue-qvalue table... 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 18:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.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 18:53:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:53:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:53:47: 1000000 INFO @ Sun, 21 Jun 2020 18:53:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:51: 2000000 INFO @ Sun, 21 Jun 2020 18:53:56: 3000000 INFO @ Sun, 21 Jun 2020 18:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.05_summits.bed INFO @ Sun, 21 Jun 2020 18:53:57: Done! pass1 - making usageList (675 chroms): 3 millis pass2 - checking and writing primary data (14817 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:02: 4000000 INFO @ Sun, 21 Jun 2020 18:54:07: 5000000 INFO @ Sun, 21 Jun 2020 18:54:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:07: #1 total tags in treatment: 5147149 INFO @ Sun, 21 Jun 2020 18:54:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:07: #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 18:54:08: #1 tags after filtering in treatment: 5146983 INFO @ Sun, 21 Jun 2020 18:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:09: #2 number of paired peaks: 653 WARNING @ Sun, 21 Jun 2020 18:54:09: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:09: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:09: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:09: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 18:54:09: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 18:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.10_model.r WARNING @ Sun, 21 Jun 2020 18:54:09: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:09: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 18:54:09: #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 18:54:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:09: #3 Pre-compute pvalue-qvalue table... 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 18:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.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 18:54:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:16: 1000000 INFO @ Sun, 21 Jun 2020 18:54:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:54:21: 2000000 INFO @ Sun, 21 Jun 2020 18:54:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.10_summits.bed INFO @ Sun, 21 Jun 2020 18:54:25: Done! pass1 - making usageList (453 chroms): 2 millis pass2 - checking and writing primary data (9499 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:54:26: 3000000 INFO @ Sun, 21 Jun 2020 18:54:32: 4000000 INFO @ Sun, 21 Jun 2020 18:54:37: 5000000 INFO @ Sun, 21 Jun 2020 18:54:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:54:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:54:38: #1 total tags in treatment: 5147149 INFO @ Sun, 21 Jun 2020 18:54:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:54:38: #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 18:54:38: #1 tags after filtering in treatment: 5146983 INFO @ Sun, 21 Jun 2020 18:54:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:54:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:54:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:54:39: #2 number of paired peaks: 653 WARNING @ Sun, 21 Jun 2020 18:54:39: Fewer paired peaks (653) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 653 pairs to build model! INFO @ Sun, 21 Jun 2020 18:54:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:54:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:54:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:54:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:54:39: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 18:54:39: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 18:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.20_model.r WARNING @ Sun, 21 Jun 2020 18:54:39: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:54:39: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 18:54:39: #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 18:54:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:54:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:54:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592428/SRX2592428.20_summits.bed INFO @ Sun, 21 Jun 2020 18:54:56: Done! pass1 - making usageList (234 chroms): 2 millis pass2 - checking and writing primary data (3765 records, 4 fields): 11 millis CompletedMACS2peakCalling