Job ID = 6459073 SRX = SRX6386750 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:55:11 prefetch.2.10.7: 1) Downloading 'SRR9624482'... 2020-06-21T12:55:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:57:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:57:47 prefetch.2.10.7: 'SRR9624482' is valid 2020-06-21T12:57:47 prefetch.2.10.7: 1) 'SRR9624482' was downloaded successfully Read 11920596 spots for SRR9624482/SRR9624482.sra Written 11920596 spots for SRR9624482/SRR9624482.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:50 11920596 reads; of these: 11920596 (100.00%) were unpaired; of these: 8337975 (69.95%) aligned 0 times 2634131 (22.10%) aligned exactly 1 time 948490 (7.96%) aligned >1 times 30.05% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 1218321 / 3582621 = 0.3401 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 22:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.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 22:01:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:01:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:01:36: 1000000 INFO @ Sun, 21 Jun 2020 22:01:42: 2000000 INFO @ Sun, 21 Jun 2020 22:01:44: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:01:44: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:01:44: #1 total tags in treatment: 2364300 INFO @ Sun, 21 Jun 2020 22:01:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:01:44: #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 22:01:44: #1 tags after filtering in treatment: 2364100 INFO @ Sun, 21 Jun 2020 22:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:01:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:01:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:01:45: #2 number of paired peaks: 1271 INFO @ Sun, 21 Jun 2020 22:01:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:01:45: start X-correlation... INFO @ Sun, 21 Jun 2020 22:01:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:01:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:01:45: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:01:45: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 22:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.05_model.r WARNING @ Sun, 21 Jun 2020 22:01:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:01:45: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 22:01:45: #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 22:01:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:01:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.05_summits.bed INFO @ Sun, 21 Jun 2020 22:01:53: Done! pass1 - making usageList (517 chroms): 2 millis pass2 - checking and writing primary data (1572 records, 4 fields): 15 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 22:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.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 22:02:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:06: 1000000 INFO @ Sun, 21 Jun 2020 22:02:13: 2000000 INFO @ Sun, 21 Jun 2020 22:02:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:02:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:02:15: #1 total tags in treatment: 2364300 INFO @ Sun, 21 Jun 2020 22:02:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:15: #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 22:02:15: #1 tags after filtering in treatment: 2364100 INFO @ Sun, 21 Jun 2020 22:02:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:15: #2 number of paired peaks: 1271 INFO @ Sun, 21 Jun 2020 22:02:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:15: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:02:15: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 22:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.10_model.r WARNING @ Sun, 21 Jun 2020 22:02:15: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:15: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 22:02:15: #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 22:02:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.10_summits.bed INFO @ Sun, 21 Jun 2020 22:02:23: Done! pass1 - making usageList (322 chroms): 0 millis pass2 - checking and writing primary data (654 records, 4 fields): 11 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 22:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.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 22:02:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:02:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:02:36: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:02:42: 2000000 INFO @ Sun, 21 Jun 2020 22:02:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:02:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:02:45: #1 total tags in treatment: 2364300 INFO @ Sun, 21 Jun 2020 22:02:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:02:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:02:45: #1 tags after filtering in treatment: 2364100 INFO @ Sun, 21 Jun 2020 22:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:02:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:02:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:02:45: #2 number of paired peaks: 1271 INFO @ Sun, 21 Jun 2020 22:02:45: start model_add_line... INFO @ Sun, 21 Jun 2020 22:02:45: start X-correlation... INFO @ Sun, 21 Jun 2020 22:02:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:02:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:02:45: #2 predicted fragment length is 57 bps INFO @ Sun, 21 Jun 2020 22:02:45: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 21 Jun 2020 22:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.20_model.r WARNING @ Sun, 21 Jun 2020 22:02:45: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:02:45: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 21 Jun 2020 22:02:45: #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 22:02:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:02:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:02:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:02:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:02:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:02:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386750/SRX6386750.20_summits.bed INFO @ Sun, 21 Jun 2020 22:02:54: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 4 millis CompletedMACS2peakCalling