Job ID = 6454623 SRX = SRX2417580 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:18:09 prefetch.2.10.7: 1) Downloading 'SRR5101092'... 2020-06-21T09:18:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:20:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:20:32 prefetch.2.10.7: 'SRR5101092' is valid 2020-06-21T09:20:32 prefetch.2.10.7: 1) 'SRR5101092' was downloaded successfully Read 18686024 spots for SRR5101092/SRR5101092.sra Written 18686024 spots for SRR5101092/SRR5101092.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: 00:06:23 18686024 reads; of these: 18686024 (100.00%) were unpaired; of these: 2799913 (14.98%) aligned 0 times 7483514 (40.05%) aligned exactly 1 time 8402597 (44.97%) aligned >1 times 85.02% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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] 3111695 / 15886111 = 0.1959 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 18:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.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 18:31:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:34: 1000000 INFO @ Sun, 21 Jun 2020 18:31:40: 2000000 INFO @ Sun, 21 Jun 2020 18:31:46: 3000000 INFO @ Sun, 21 Jun 2020 18:31:52: 4000000 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 18:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.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 18:31:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:58: 5000000 INFO @ Sun, 21 Jun 2020 18:32:04: 1000000 INFO @ Sun, 21 Jun 2020 18:32:05: 6000000 INFO @ Sun, 21 Jun 2020 18:32:10: 2000000 INFO @ Sun, 21 Jun 2020 18:32:11: 7000000 INFO @ Sun, 21 Jun 2020 18:32:17: 3000000 INFO @ Sun, 21 Jun 2020 18:32:18: 8000000 INFO @ Sun, 21 Jun 2020 18:32:23: 4000000 INFO @ Sun, 21 Jun 2020 18:32:24: 9000000 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 18:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.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 18:32:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:29: 5000000 INFO @ Sun, 21 Jun 2020 18:32:30: 10000000 INFO @ Sun, 21 Jun 2020 18:32:34: 1000000 INFO @ Sun, 21 Jun 2020 18:32:36: 6000000 INFO @ Sun, 21 Jun 2020 18:32:37: 11000000 INFO @ Sun, 21 Jun 2020 18:32:41: 2000000 INFO @ Sun, 21 Jun 2020 18:32:43: 7000000 INFO @ Sun, 21 Jun 2020 18:32:43: 12000000 INFO @ Sun, 21 Jun 2020 18:32:47: 3000000 INFO @ Sun, 21 Jun 2020 18:32:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:32:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:32:49: #1 total tags in treatment: 12774416 INFO @ Sun, 21 Jun 2020 18:32:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:32:49: #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 18:32:49: #1 tags after filtering in treatment: 12774365 INFO @ Sun, 21 Jun 2020 18:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:32:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:32:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:32:49: 8000000 INFO @ Sun, 21 Jun 2020 18:32:50: #2 number of paired peaks: 2634 INFO @ Sun, 21 Jun 2020 18:32:50: start model_add_line... INFO @ Sun, 21 Jun 2020 18:32:50: start X-correlation... INFO @ Sun, 21 Jun 2020 18:32:50: end of X-cor INFO @ Sun, 21 Jun 2020 18:32:50: #2 finished! INFO @ Sun, 21 Jun 2020 18:32:50: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:32:50: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 18:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.05_model.r WARNING @ Sun, 21 Jun 2020 18:32:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:32:50: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 18:32:50: #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 18:32:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:32:54: 4000000 INFO @ Sun, 21 Jun 2020 18:32:56: 9000000 INFO @ Sun, 21 Jun 2020 18:33:00: 5000000 INFO @ Sun, 21 Jun 2020 18:33:02: 10000000 INFO @ Sun, 21 Jun 2020 18:33:07: 6000000 INFO @ Sun, 21 Jun 2020 18:33:09: 11000000 INFO @ Sun, 21 Jun 2020 18:33:14: 7000000 INFO @ Sun, 21 Jun 2020 18:33:16: 12000000 INFO @ Sun, 21 Jun 2020 18:33:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:20: 8000000 INFO @ Sun, 21 Jun 2020 18:33:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:21: #1 total tags in treatment: 12774416 INFO @ Sun, 21 Jun 2020 18:33:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:21: #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 18:33:21: #1 tags after filtering in treatment: 12774365 INFO @ Sun, 21 Jun 2020 18:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:23: #2 number of paired peaks: 2634 INFO @ Sun, 21 Jun 2020 18:33:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:23: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:33:23: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 18:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:23: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 18:33:23: #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 18:33:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:27: 9000000 INFO @ Sun, 21 Jun 2020 18:33:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:33:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:33:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.05_summits.bed INFO @ Sun, 21 Jun 2020 18:33:32: Done! pass1 - making usageList (836 chroms): 1 millis pass2 - checking and writing primary data (3971 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:33:33: 10000000 INFO @ Sun, 21 Jun 2020 18:33:40: 11000000 INFO @ Sun, 21 Jun 2020 18:33:45: 12000000 INFO @ Sun, 21 Jun 2020 18:33:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:50: #1 total tags in treatment: 12774416 INFO @ Sun, 21 Jun 2020 18:33:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:50: #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 18:33:51: #1 tags after filtering in treatment: 12774365 INFO @ Sun, 21 Jun 2020 18:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:51: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:52: #2 number of paired peaks: 2634 INFO @ Sun, 21 Jun 2020 18:33:52: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:52: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:52: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:52: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:52: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 18:33:52: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 21 Jun 2020 18:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.20_model.r WARNING @ Sun, 21 Jun 2020 18:33:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:52: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 21 Jun 2020 18:33:52: #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 18:33:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:03: Done! pass1 - making usageList (710 chroms): 2 millis pass2 - checking and writing primary data (2758 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2417580/SRX2417580.20_summits.bed INFO @ Sun, 21 Jun 2020 18:34:32: Done! pass1 - making usageList (532 chroms): 1 millis pass2 - checking and writing primary data (1760 records, 4 fields): 17 millis CompletedMACS2peakCalling