Job ID = 6459048 SRX = SRX6386729 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:56:51 prefetch.2.10.7: 1) Downloading 'SRR9624461'... 2020-06-21T12:56:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:58:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:58:43 prefetch.2.10.7: 'SRR9624461' is valid 2020-06-21T12:58:43 prefetch.2.10.7: 1) 'SRR9624461' was downloaded successfully Read 10534288 spots for SRR9624461/SRR9624461.sra Written 10534288 spots for SRR9624461/SRR9624461.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: 00:02:05 10534288 reads; of these: 10534288 (100.00%) were unpaired; of these: 4478311 (42.51%) aligned 0 times 4372931 (41.51%) aligned exactly 1 time 1683046 (15.98%) aligned >1 times 57.49% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 1714086 / 6055977 = 0.2830 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 22:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.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 22:03:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:31: 1000000 INFO @ Sun, 21 Jun 2020 22:03:38: 2000000 INFO @ Sun, 21 Jun 2020 22:03:45: 3000000 INFO @ Sun, 21 Jun 2020 22:03:52: 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 @ Sun, 21 Jun 2020 22:03:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.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 22:03:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:03:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:03:55: #1 total tags in treatment: 4341891 INFO @ Sun, 21 Jun 2020 22:03:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:03:55: #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 22:03:55: #1 tags after filtering in treatment: 4341883 INFO @ Sun, 21 Jun 2020 22:03:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:03:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:03:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:03:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:03:56: #2 number of paired peaks: 883 WARNING @ Sun, 21 Jun 2020 22:03:56: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sun, 21 Jun 2020 22:03:56: start model_add_line... INFO @ Sun, 21 Jun 2020 22:03:56: start X-correlation... INFO @ Sun, 21 Jun 2020 22:03:56: end of X-cor INFO @ Sun, 21 Jun 2020 22:03:56: #2 finished! INFO @ Sun, 21 Jun 2020 22:03:56: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 22:03:56: #2 alternative fragment length(s) may be 60,570 bps INFO @ Sun, 21 Jun 2020 22:03:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.05_model.r WARNING @ Sun, 21 Jun 2020 22:03:56: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:03:56: #2 You may need to consider one of the other alternative d(s): 60,570 WARNING @ Sun, 21 Jun 2020 22:03:56: #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 22:03:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:03:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:02: 1000000 INFO @ Sun, 21 Jun 2020 22:04:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:08: 2000000 INFO @ Sun, 21 Jun 2020 22:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.05_summits.bed INFO @ Sun, 21 Jun 2020 22:04:11: Done! pass1 - making usageList (592 chroms): 1 millis pass2 - checking and writing primary data (1845 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:15: 3000000 INFO @ Sun, 21 Jun 2020 22:04:22: 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 @ Sun, 21 Jun 2020 22:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.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 22:04:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:04:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:04:25: #1 total tags in treatment: 4341891 INFO @ Sun, 21 Jun 2020 22:04:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:25: #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 22:04:25: #1 tags after filtering in treatment: 4341883 INFO @ Sun, 21 Jun 2020 22:04:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:25: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:25: #2 number of paired peaks: 883 WARNING @ Sun, 21 Jun 2020 22:04:25: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:25: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 22:04:25: #2 alternative fragment length(s) may be 60,570 bps INFO @ Sun, 21 Jun 2020 22:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.10_model.r WARNING @ Sun, 21 Jun 2020 22:04:25: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:25: #2 You may need to consider one of the other alternative d(s): 60,570 WARNING @ Sun, 21 Jun 2020 22:04:25: #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 22:04:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:31: 1000000 INFO @ Sun, 21 Jun 2020 22:04:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:04:36: 2000000 INFO @ Sun, 21 Jun 2020 22:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.10_summits.bed INFO @ Sun, 21 Jun 2020 22:04:40: Done! pass1 - making usageList (305 chroms): 2 millis pass2 - checking and writing primary data (607 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:04:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:04:48: 4000000 INFO @ Sun, 21 Jun 2020 22:04:50: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:04:50: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:04:50: #1 total tags in treatment: 4341891 INFO @ Sun, 21 Jun 2020 22:04:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:50: #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 22:04:51: #1 tags after filtering in treatment: 4341883 INFO @ Sun, 21 Jun 2020 22:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:51: #2 number of paired peaks: 883 WARNING @ Sun, 21 Jun 2020 22:04:51: Fewer paired peaks (883) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 883 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:51: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:51: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:51: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:51: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:51: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 22:04:51: #2 alternative fragment length(s) may be 60,570 bps INFO @ Sun, 21 Jun 2020 22:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.20_model.r WARNING @ Sun, 21 Jun 2020 22:04:51: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:51: #2 You may need to consider one of the other alternative d(s): 60,570 WARNING @ Sun, 21 Jun 2020 22:04:51: #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 22:04:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:05:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386729/SRX6386729.20_summits.bed INFO @ Sun, 21 Jun 2020 22:05:06: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 6 millis CompletedMACS2peakCalling