Job ID = 6454000 SRX = SRX1760704 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:50:19 prefetch.2.10.7: 1) Downloading 'SRR3503065'... 2020-06-21T08:50:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:51:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:51:56 prefetch.2.10.7: 'SRR3503065' is valid 2020-06-21T08:51:56 prefetch.2.10.7: 1) 'SRR3503065' was downloaded successfully 2020-06-21T08:51:56 prefetch.2.10.7: 'SRR3503065' has 0 unresolved dependencies Read 4878566 spots for SRR3503065/SRR3503065.sra Written 4878566 spots for SRR3503065/SRR3503065.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: 00:05:37 4878566 reads; of these: 4878566 (100.00%) were unpaired; of these: 1301782 (26.68%) aligned 0 times 1869438 (38.32%) aligned exactly 1 time 1707346 (35.00%) aligned >1 times 73.32% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 287007 / 3576784 = 0.0802 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 18:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.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 18:00:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:28: 1000000 INFO @ Sun, 21 Jun 2020 18:00:36: 2000000 INFO @ Sun, 21 Jun 2020 18:00:45: 3000000 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 18:00:48: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:00:48: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:00:48: #1 total tags in treatment: 3289777 INFO @ Sun, 21 Jun 2020 18:00:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:48: #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 18:00:48: #1 tags after filtering in treatment: 3289567 INFO @ Sun, 21 Jun 2020 18:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:48: #2 number of paired peaks: 2769 INFO @ Sun, 21 Jun 2020 18:00:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:48: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:48: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:48: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:48: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 18:00:48: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 18:00:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.05_model.r WARNING @ Sun, 21 Jun 2020 18:00:48: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:00:48: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 18:00:48: #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 18:00:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.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 18:00:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:00:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:00:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:00: 1000000 INFO @ Sun, 21 Jun 2020 18:01:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:01: Done! pass1 - making usageList (726 chroms): 1 millis pass2 - checking and writing primary data (2086 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:01:11: 2000000 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 18:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.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 18:01:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:01:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:01:22: 3000000 INFO @ Sun, 21 Jun 2020 18:01:25: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:01:25: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:01:25: #1 total tags in treatment: 3289777 INFO @ Sun, 21 Jun 2020 18:01:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:25: #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 18:01:26: #1 tags after filtering in treatment: 3289567 INFO @ Sun, 21 Jun 2020 18:01:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:26: #2 number of paired peaks: 2769 INFO @ Sun, 21 Jun 2020 18:01:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:26: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 18:01:26: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 18:01:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.10_model.r WARNING @ Sun, 21 Jun 2020 18:01:26: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:26: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 18:01:26: #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 18:01:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:01:31: 1000000 INFO @ Sun, 21 Jun 2020 18:01:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.10_summits.bed INFO @ Sun, 21 Jun 2020 18:01:38: Done! pass1 - making usageList (641 chroms): 1 millis pass2 - checking and writing primary data (1510 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:01:42: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:01:53: 3000000 INFO @ Sun, 21 Jun 2020 18:01:56: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:01:56: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:01:56: #1 total tags in treatment: 3289777 INFO @ Sun, 21 Jun 2020 18:01:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:56: #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 18:01:56: #1 tags after filtering in treatment: 3289567 INFO @ Sun, 21 Jun 2020 18:01:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:56: #2 number of paired peaks: 2769 INFO @ Sun, 21 Jun 2020 18:01:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:56: #2 predicted fragment length is 143 bps INFO @ Sun, 21 Jun 2020 18:01:56: #2 alternative fragment length(s) may be 143 bps INFO @ Sun, 21 Jun 2020 18:01:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.20_model.r WARNING @ Sun, 21 Jun 2020 18:01:56: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:01:56: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Sun, 21 Jun 2020 18:01:56: #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 18:01:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:02:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760704/SRX1760704.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:09: Done! pass1 - making usageList (513 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 14 millis CompletedMACS2peakCalling