Job ID = 6458010 SRX = SRX4933912 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:02:35 prefetch.2.10.7: 1) Downloading 'SRR8107303'... 2020-06-21T12:02:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:05:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:05:07 prefetch.2.10.7: 'SRR8107303' is valid 2020-06-21T12:05:07 prefetch.2.10.7: 1) 'SRR8107303' was downloaded successfully Read 14479893 spots for SRR8107303/SRR8107303.sra Written 14479893 spots for SRR8107303/SRR8107303.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: 00:02:44 14479893 reads; of these: 14479893 (100.00%) were unpaired; of these: 7060919 (48.76%) aligned 0 times 5822012 (40.21%) aligned exactly 1 time 1596962 (11.03%) aligned >1 times 51.24% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 6048900 / 7418974 = 0.8153 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 21:10:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.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 21:10:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:28: 1000000 INFO @ Sun, 21 Jun 2020 21:10:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:10:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:10:31: #1 total tags in treatment: 1370074 INFO @ Sun, 21 Jun 2020 21:10:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:10:31: #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 21:10:31: #1 tags after filtering in treatment: 1369894 INFO @ Sun, 21 Jun 2020 21:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:10:31: #1 finished! INFO @ Sun, 21 Jun 2020 21:10:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:10:31: #2 number of paired peaks: 3328 INFO @ Sun, 21 Jun 2020 21:10:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:10:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:10:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:10:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:10:31: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 21:10:31: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 21:10:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.05_model.r WARNING @ Sun, 21 Jun 2020 21:10:31: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:10:31: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 21 Jun 2020 21:10:31: #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 21:10:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:10:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:10:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.05_summits.bed INFO @ Sun, 21 Jun 2020 21:10:36: Done! pass1 - making usageList (488 chroms): 1 millis pass2 - checking and writing primary data (1187 records, 4 fields): 45 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 @ Sun, 21 Jun 2020 21:10:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.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 21:10:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:10:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:10:58: 1000000 INFO @ Sun, 21 Jun 2020 21:11:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:11:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:11:00: #1 total tags in treatment: 1370074 INFO @ Sun, 21 Jun 2020 21:11:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:11:00: #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 21:11:00: #1 tags after filtering in treatment: 1369894 INFO @ Sun, 21 Jun 2020 21:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:11:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:11:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:11:00: #2 number of paired peaks: 3328 INFO @ Sun, 21 Jun 2020 21:11:00: start model_add_line... INFO @ Sun, 21 Jun 2020 21:11:00: start X-correlation... INFO @ Sun, 21 Jun 2020 21:11:00: end of X-cor INFO @ Sun, 21 Jun 2020 21:11:00: #2 finished! INFO @ Sun, 21 Jun 2020 21:11:00: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 21:11:00: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 21:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.10_model.r WARNING @ Sun, 21 Jun 2020 21:11:00: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:11:00: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 21 Jun 2020 21:11:00: #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 21:11:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:11:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:11:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.10_summits.bed INFO @ Sun, 21 Jun 2020 21:11:06: Done! pass1 - making usageList (233 chroms): 1 millis pass2 - checking and writing primary data (451 records, 4 fields): 8 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 @ Sun, 21 Jun 2020 21:11:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.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 21:11:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:11:21: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:11:28: 1000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:11:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:11:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:11:30: #1 total tags in treatment: 1370074 INFO @ Sun, 21 Jun 2020 21:11:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:11:30: #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 21:11:30: #1 tags after filtering in treatment: 1369894 INFO @ Sun, 21 Jun 2020 21:11:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:11:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:11:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:11:31: #2 number of paired peaks: 3328 INFO @ Sun, 21 Jun 2020 21:11:31: start model_add_line... INFO @ Sun, 21 Jun 2020 21:11:31: start X-correlation... INFO @ Sun, 21 Jun 2020 21:11:31: end of X-cor INFO @ Sun, 21 Jun 2020 21:11:31: #2 finished! INFO @ Sun, 21 Jun 2020 21:11:31: #2 predicted fragment length is 97 bps INFO @ Sun, 21 Jun 2020 21:11:31: #2 alternative fragment length(s) may be 97 bps INFO @ Sun, 21 Jun 2020 21:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.20_model.r WARNING @ Sun, 21 Jun 2020 21:11:31: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:11:31: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Sun, 21 Jun 2020 21:11:31: #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 21:11:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:11:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933912/SRX4933912.20_summits.bed INFO @ Sun, 21 Jun 2020 21:11:36: Done! pass1 - making usageList (110 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 5 millis CompletedMACS2peakCalling