Job ID = 6453630 SRX = SRX1308480 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:25:56 prefetch.2.10.7: 1) Downloading 'SRR2566771'... 2020-06-21T08:25:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:28:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:28:44 prefetch.2.10.7: 'SRR2566771' is valid 2020-06-21T08:28:44 prefetch.2.10.7: 1) 'SRR2566771' was downloaded successfully Read 8947712 spots for SRR2566771/SRR2566771.sra Written 8947712 spots for SRR2566771/SRR2566771.sra 2020-06-21T08:29:23 prefetch.2.10.7: 1) Downloading 'SRR2566772'... 2020-06-21T08:29:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:14 prefetch.2.10.7: 'SRR2566772' is valid 2020-06-21T08:31:14 prefetch.2.10.7: 1) 'SRR2566772' was downloaded successfully Read 8944573 spots for SRR2566772/SRR2566772.sra Written 8944573 spots for SRR2566772/SRR2566772.sra 2020-06-21T08:31:51 prefetch.2.10.7: 1) Downloading 'SRR2566773'... 2020-06-21T08:31:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:36 prefetch.2.10.7: 'SRR2566773' is valid 2020-06-21T08:33:36 prefetch.2.10.7: 1) 'SRR2566773' was downloaded successfully Read 10727054 spots for SRR2566773/SRR2566773.sra Written 10727054 spots for SRR2566773/SRR2566773.sra 2020-06-21T08:34:17 prefetch.2.10.7: 1) Downloading 'SRR2566774'... 2020-06-21T08:34:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:43 prefetch.2.10.7: 'SRR2566774' is valid 2020-06-21T08:36:43 prefetch.2.10.7: 1) 'SRR2566774' was downloaded successfully Read 10730402 spots for SRR2566774/SRR2566774.sra Written 10730402 spots for SRR2566774/SRR2566774.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: 00:09:06 39349741 reads; of these: 39349741 (100.00%) were unpaired; of these: 4343580 (11.04%) aligned 0 times 29217703 (74.25%) aligned exactly 1 time 5788458 (14.71%) aligned >1 times 88.96% overall alignment rate Time searching: 00:09:06 Overall time: 00:09:06 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_sort_core] merging from 16 files... [bam_rmdupse_core] 31147223 / 35006161 = 0.8898 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 17:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.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 17:52:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:15: 1000000 INFO @ Sun, 21 Jun 2020 17:52:20: 2000000 INFO @ Sun, 21 Jun 2020 17:52:26: 3000000 INFO @ Sun, 21 Jun 2020 17:52:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:52:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:52:31: #1 total tags in treatment: 3858938 INFO @ Sun, 21 Jun 2020 17:52:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:52:31: #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 17:52:31: #1 tags after filtering in treatment: 3858885 INFO @ Sun, 21 Jun 2020 17:52:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:52:31: #1 finished! INFO @ Sun, 21 Jun 2020 17:52:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:52:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:52:31: #2 number of paired peaks: 2852 INFO @ Sun, 21 Jun 2020 17:52:31: start model_add_line... INFO @ Sun, 21 Jun 2020 17:52:31: start X-correlation... INFO @ Sun, 21 Jun 2020 17:52:31: end of X-cor INFO @ Sun, 21 Jun 2020 17:52:31: #2 finished! INFO @ Sun, 21 Jun 2020 17:52:31: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 17:52:31: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 17:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.05_model.r WARNING @ Sun, 21 Jun 2020 17:52:31: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:52:31: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 17:52:31: #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 17:52:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:52:31: #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 17:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.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 17:52:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:52:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:52:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.05_summits.bed INFO @ Sun, 21 Jun 2020 17:52:44: Done! pass1 - making usageList (710 chroms): 2 millis pass2 - checking and writing primary data (5578 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:52:45: 1000000 INFO @ Sun, 21 Jun 2020 17:52:50: 2000000 INFO @ Sun, 21 Jun 2020 17:52:56: 3000000 INFO @ Sun, 21 Jun 2020 17:53:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:01: #1 total tags in treatment: 3858938 INFO @ Sun, 21 Jun 2020 17:53:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:01: #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 17:53:01: #1 tags after filtering in treatment: 3858885 INFO @ Sun, 21 Jun 2020 17:53:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:01: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:01: #2 number of paired peaks: 2852 INFO @ Sun, 21 Jun 2020 17:53:01: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:02: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:02: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:02: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:02: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 17:53:02: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 17:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.10_model.r WARNING @ Sun, 21 Jun 2020 17:53:02: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:02: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 17:53:02: #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 17:53:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:02: #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 17:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.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 17:53:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.10_summits.bed INFO @ Sun, 21 Jun 2020 17:53:15: Done! pass1 - making usageList (521 chroms): 2 millis pass2 - checking and writing primary data (2748 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:53:16: 1000000 INFO @ Sun, 21 Jun 2020 17:53:23: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:53:29: 3000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:53:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:53:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:53:35: #1 total tags in treatment: 3858938 INFO @ Sun, 21 Jun 2020 17:53:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:53:35: #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 17:53:35: #1 tags after filtering in treatment: 3858885 INFO @ Sun, 21 Jun 2020 17:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:53:35: #1 finished! INFO @ Sun, 21 Jun 2020 17:53:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:53:36: #2 number of paired peaks: 2852 INFO @ Sun, 21 Jun 2020 17:53:36: start model_add_line... INFO @ Sun, 21 Jun 2020 17:53:36: start X-correlation... INFO @ Sun, 21 Jun 2020 17:53:36: end of X-cor INFO @ Sun, 21 Jun 2020 17:53:36: #2 finished! INFO @ Sun, 21 Jun 2020 17:53:36: #2 predicted fragment length is 72 bps INFO @ Sun, 21 Jun 2020 17:53:36: #2 alternative fragment length(s) may be 72 bps INFO @ Sun, 21 Jun 2020 17:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.20_model.r WARNING @ Sun, 21 Jun 2020 17:53:36: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:53:36: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sun, 21 Jun 2020 17:53:36: #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 17:53:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:53:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308480/SRX1308480.20_summits.bed INFO @ Sun, 21 Jun 2020 17:53:48: Done! pass1 - making usageList (434 chroms): 1 millis pass2 - checking and writing primary data (1331 records, 4 fields): 16 millis CompletedMACS2peakCalling