Job ID = 6457061 SRX = SRX4375828 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:25:09 prefetch.2.10.7: 1) Downloading 'SRR7506482'... 2020-06-21T11:25:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:21 prefetch.2.10.7: 'SRR7506482' is valid 2020-06-21T11:26:21 prefetch.2.10.7: 1) 'SRR7506482' was downloaded successfully Read 7489836 spots for SRR7506482/SRR7506482.sra Written 7489836 spots for SRR7506482/SRR7506482.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: 00:01:38 7489836 reads; of these: 7489836 (100.00%) were unpaired; of these: 2179312 (29.10%) aligned 0 times 4026871 (53.76%) aligned exactly 1 time 1283653 (17.14%) aligned >1 times 70.90% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 919326 / 5310524 = 0.1731 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 20:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.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 20:30:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:27: 1000000 INFO @ Sun, 21 Jun 2020 20:30:33: 2000000 INFO @ Sun, 21 Jun 2020 20:30:38: 3000000 INFO @ Sun, 21 Jun 2020 20:30:44: 4000000 INFO @ Sun, 21 Jun 2020 20:30:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:30:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:30:47: #1 total tags in treatment: 4391198 INFO @ Sun, 21 Jun 2020 20:30:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:30:47: #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 20:30:47: #1 tags after filtering in treatment: 4390980 INFO @ Sun, 21 Jun 2020 20:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:30:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:30:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:30:48: #2 number of paired peaks: 1046 INFO @ Sun, 21 Jun 2020 20:30:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:30:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:30:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:30:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:30:48: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 20:30:48: #2 alternative fragment length(s) may be 69 bps INFO @ Sun, 21 Jun 2020 20:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.05_model.r WARNING @ Sun, 21 Jun 2020 20:30:48: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:30:48: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sun, 21 Jun 2020 20:30:48: #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 20:30:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:30:48: #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 20:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.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 20:30:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:30:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:30:57: 1000000 INFO @ Sun, 21 Jun 2020 20:30:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:03: 2000000 INFO @ Sun, 21 Jun 2020 20:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.05_summits.bed INFO @ Sun, 21 Jun 2020 20:31:05: Done! pass1 - making usageList (530 chroms): 2 millis pass2 - checking and writing primary data (1752 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:31:08: 3000000 INFO @ Sun, 21 Jun 2020 20:31:14: 4000000 INFO @ Sun, 21 Jun 2020 20:31:17: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:17: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:17: #1 total tags in treatment: 4391198 INFO @ Sun, 21 Jun 2020 20:31:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:17: #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 20:31:17: #1 tags after filtering in treatment: 4390980 INFO @ Sun, 21 Jun 2020 20:31:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:17: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:17: #2 number of paired peaks: 1046 INFO @ Sun, 21 Jun 2020 20:31:17: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:17: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:17: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:17: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:17: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 20:31:17: #2 alternative fragment length(s) may be 69 bps INFO @ Sun, 21 Jun 2020 20:31:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.10_model.r WARNING @ Sun, 21 Jun 2020 20:31:17: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:31:17: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sun, 21 Jun 2020 20:31:17: #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 20:31:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:17: #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 20:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.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 20:31:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:31:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:31:27: 1000000 INFO @ Sun, 21 Jun 2020 20:31:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:31:33: 2000000 INFO @ Sun, 21 Jun 2020 20:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.10_summits.bed INFO @ Sun, 21 Jun 2020 20:31:34: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:31:38: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:31:44: 4000000 INFO @ Sun, 21 Jun 2020 20:31:47: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:31:47: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:31:47: #1 total tags in treatment: 4391198 INFO @ Sun, 21 Jun 2020 20:31:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:31:47: #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 20:31:47: #1 tags after filtering in treatment: 4390980 INFO @ Sun, 21 Jun 2020 20:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:31:47: #1 finished! INFO @ Sun, 21 Jun 2020 20:31:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:31:48: #2 number of paired peaks: 1046 INFO @ Sun, 21 Jun 2020 20:31:48: start model_add_line... INFO @ Sun, 21 Jun 2020 20:31:48: start X-correlation... INFO @ Sun, 21 Jun 2020 20:31:48: end of X-cor INFO @ Sun, 21 Jun 2020 20:31:48: #2 finished! INFO @ Sun, 21 Jun 2020 20:31:48: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 20:31:48: #2 alternative fragment length(s) may be 69 bps INFO @ Sun, 21 Jun 2020 20:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.20_model.r WARNING @ Sun, 21 Jun 2020 20:31:48: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:31:48: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Sun, 21 Jun 2020 20:31:48: #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 20:31:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:31:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:31:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375828/SRX4375828.20_summits.bed INFO @ Sun, 21 Jun 2020 20:32:04: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 7 millis CompletedMACS2peakCalling