Job ID = 6509077 SRX = SRX645120 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:56:59 prefetch.2.10.7: 1) Downloading 'SRR1505720'... 2020-06-26T14:56:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:59:02 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:59:02 prefetch.2.10.7: 1) 'SRR1505720' was downloaded successfully Read 11183254 spots for SRR1505720/SRR1505720.sra Written 11183254 spots for SRR1505720/SRR1505720.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: 00:04:03 11183254 reads; of these: 11183254 (100.00%) were unpaired; of these: 6762438 (60.47%) aligned 0 times 3128744 (27.98%) aligned exactly 1 time 1292072 (11.55%) aligned >1 times 39.53% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 3481456 / 4420816 = 0.7875 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 @ Sat, 27 Jun 2020 00:05:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.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 @ Sat, 27 Jun 2020 00:05:27: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:05:27: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:05:35: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:05:35: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:05:35: #1 total tags in treatment: 939360 INFO @ Sat, 27 Jun 2020 00:05:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:05:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:05:35: #1 tags after filtering in treatment: 939133 INFO @ Sat, 27 Jun 2020 00:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:05:35: #1 finished! INFO @ Sat, 27 Jun 2020 00:05:35: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:05:36: #2 number of paired peaks: 2453 INFO @ Sat, 27 Jun 2020 00:05:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:05:36: start X-correlation... INFO @ Sat, 27 Jun 2020 00:05:36: end of X-cor INFO @ Sat, 27 Jun 2020 00:05:36: #2 finished! INFO @ Sat, 27 Jun 2020 00:05:36: #2 predicted fragment length is 103 bps INFO @ Sat, 27 Jun 2020 00:05:36: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 27 Jun 2020 00:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.05_model.r WARNING @ Sat, 27 Jun 2020 00:05:36: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:05:36: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 27 Jun 2020 00:05:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:05:36: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:05:39: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:05:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:05:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:05:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.05_summits.bed INFO @ Sat, 27 Jun 2020 00:05:40: Done! pass1 - making usageList (559 chroms): 1 millis pass2 - checking and writing primary data (1159 records, 4 fields): 18 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 @ Sat, 27 Jun 2020 00:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.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 @ Sat, 27 Jun 2020 00:05:57: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:05:57: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:06:05: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:06:05: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:06:05: #1 total tags in treatment: 939360 INFO @ Sat, 27 Jun 2020 00:06:05: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:06:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:06:05: #1 tags after filtering in treatment: 939133 INFO @ Sat, 27 Jun 2020 00:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:06:05: #1 finished! INFO @ Sat, 27 Jun 2020 00:06:05: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:06:06: #2 number of paired peaks: 2453 INFO @ Sat, 27 Jun 2020 00:06:06: start model_add_line... INFO @ Sat, 27 Jun 2020 00:06:06: start X-correlation... INFO @ Sat, 27 Jun 2020 00:06:06: end of X-cor INFO @ Sat, 27 Jun 2020 00:06:06: #2 finished! INFO @ Sat, 27 Jun 2020 00:06:06: #2 predicted fragment length is 103 bps INFO @ Sat, 27 Jun 2020 00:06:06: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 27 Jun 2020 00:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.10_model.r WARNING @ Sat, 27 Jun 2020 00:06:06: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:06:06: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 27 Jun 2020 00:06:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:06:06: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:06:09: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.10_summits.bed INFO @ Sat, 27 Jun 2020 00:06:10: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (622 records, 4 fields): 18 millis CompletedMACS2peakCalling 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 @ Sat, 27 Jun 2020 00:06:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.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 @ Sat, 27 Jun 2020 00:06:27: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:06:27: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:06:35: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:06:35: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:06:35: #1 total tags in treatment: 939360 INFO @ Sat, 27 Jun 2020 00:06:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:06:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:06:35: #1 tags after filtering in treatment: 939133 INFO @ Sat, 27 Jun 2020 00:06:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:06:35: #1 finished! INFO @ Sat, 27 Jun 2020 00:06:35: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:06:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:06:36: #2 number of paired peaks: 2453 INFO @ Sat, 27 Jun 2020 00:06:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:06:36: start X-correlation... INFO @ Sat, 27 Jun 2020 00:06:36: end of X-cor INFO @ Sat, 27 Jun 2020 00:06:36: #2 finished! INFO @ Sat, 27 Jun 2020 00:06:36: #2 predicted fragment length is 103 bps INFO @ Sat, 27 Jun 2020 00:06:36: #2 alternative fragment length(s) may be 103 bps INFO @ Sat, 27 Jun 2020 00:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.20_model.r WARNING @ Sat, 27 Jun 2020 00:06:36: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:06:36: #2 You may need to consider one of the other alternative d(s): 103 WARNING @ Sat, 27 Jun 2020 00:06:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:06:36: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:06:39: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645120/SRX645120.20_summits.bed INFO @ Sat, 27 Jun 2020 00:06:40: Done! pass1 - making usageList (178 chroms): 2 millis pass2 - checking and writing primary data (240 records, 4 fields): 8 millis CompletedMACS2peakCalling