Job ID = 6458931 SRX = SRX5775931 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:43:25 prefetch.2.10.7: 1) Downloading 'SRR8997134'... 2020-06-21T12:43:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:46:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:46:42 prefetch.2.10.7: 1) 'SRR8997134' was downloaded successfully Read 20826584 spots for SRR8997134/SRR8997134.sra Written 20826584 spots for SRR8997134/SRR8997134.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: 00:07:17 20826584 reads; of these: 20826584 (100.00%) were unpaired; of these: 2264823 (10.87%) aligned 0 times 13457468 (64.62%) aligned exactly 1 time 5104293 (24.51%) aligned >1 times 89.13% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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 8 files... [bam_rmdupse_core] 13408467 / 18561761 = 0.7224 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 21:59:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.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 21:59:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:23: 1000000 INFO @ Sun, 21 Jun 2020 21:59:29: 2000000 INFO @ Sun, 21 Jun 2020 21:59:34: 3000000 INFO @ Sun, 21 Jun 2020 21:59:39: 4000000 INFO @ Sun, 21 Jun 2020 21:59:45: 5000000 INFO @ Sun, 21 Jun 2020 21:59:46: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:59:46: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:59:46: #1 total tags in treatment: 5153294 INFO @ Sun, 21 Jun 2020 21:59:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:46: #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 21:59:46: #1 tags after filtering in treatment: 5153286 INFO @ Sun, 21 Jun 2020 21:59:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:46: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:46: #2 looking for paired plus/minus strand peaks... 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 21:59:47: #2 number of paired peaks: 1822 INFO @ Sun, 21 Jun 2020 21:59:47: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:47: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:47: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:47: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:47: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 21:59:47: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 21 Jun 2020 21:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.05_model.r WARNING @ Sun, 21 Jun 2020 21:59:47: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:47: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sun, 21 Jun 2020 21:59:47: #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 21:59:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.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 21:59:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:59:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:59:53: 1000000 INFO @ Sun, 21 Jun 2020 21:59:58: 2000000 INFO @ Sun, 21 Jun 2020 21:59:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:03: 3000000 INFO @ Sun, 21 Jun 2020 22:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:04: Done! pass1 - making usageList (734 chroms): 1 millis pass2 - checking and writing primary data (2417 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:09: 4000000 INFO @ Sun, 21 Jun 2020 22:00:14: 5000000 INFO @ Sun, 21 Jun 2020 22:00:15: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:00:15: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:00:15: #1 total tags in treatment: 5153294 INFO @ Sun, 21 Jun 2020 22:00:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:15: #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 22:00:15: #1 tags after filtering in treatment: 5153286 INFO @ Sun, 21 Jun 2020 22:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:15: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:15: #2 number of paired peaks: 1822 INFO @ Sun, 21 Jun 2020 22:00:15: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:15: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:15: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:15: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:15: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 22:00:15: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 21 Jun 2020 22:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.10_model.r WARNING @ Sun, 21 Jun 2020 22:00:15: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:15: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sun, 21 Jun 2020 22:00:15: #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 22:00:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:15: #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 22:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.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 22:00:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:00:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:00:23: 1000000 INFO @ Sun, 21 Jun 2020 22:00:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:28: 2000000 INFO @ Sun, 21 Jun 2020 22:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:32: Done! pass1 - making usageList (605 chroms): 1 millis pass2 - checking and writing primary data (1772 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:33: 3000000 INFO @ Sun, 21 Jun 2020 22:00:39: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:00:44: 5000000 INFO @ Sun, 21 Jun 2020 22:00:45: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:00:45: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:00:45: #1 total tags in treatment: 5153294 INFO @ Sun, 21 Jun 2020 22:00:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:45: #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 22:00:45: #1 tags after filtering in treatment: 5153286 INFO @ Sun, 21 Jun 2020 22:00:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:46: #2 number of paired peaks: 1822 INFO @ Sun, 21 Jun 2020 22:00:46: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:46: #2 predicted fragment length is 74 bps INFO @ Sun, 21 Jun 2020 22:00:46: #2 alternative fragment length(s) may be 74 bps INFO @ Sun, 21 Jun 2020 22:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.20_model.r WARNING @ Sun, 21 Jun 2020 22:00:46: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:46: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sun, 21 Jun 2020 22:00:46: #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 22:00:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:00:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775931/SRX5775931.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:02: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1284 records, 4 fields): 14 millis CompletedMACS2peakCalling