Job ID = 6454427 SRX = SRX2055955 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:13:39 prefetch.2.10.7: 1) Downloading 'SRR4069187'... 2020-06-21T09:13:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:16:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:16:39 prefetch.2.10.7: 1) 'SRR4069187' was downloaded successfully Read 24593353 spots for SRR4069187/SRR4069187.sra Written 24593353 spots for SRR4069187/SRR4069187.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: 00:05:51 24593353 reads; of these: 24593353 (100.00%) were unpaired; of these: 11154462 (45.36%) aligned 0 times 8621296 (35.06%) aligned exactly 1 time 4817595 (19.59%) aligned >1 times 54.64% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3870634 / 13438891 = 0.2880 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 18:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.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 18:26:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:48: 1000000 INFO @ Sun, 21 Jun 2020 18:26:53: 2000000 INFO @ Sun, 21 Jun 2020 18:26:58: 3000000 INFO @ Sun, 21 Jun 2020 18:27:03: 4000000 INFO @ Sun, 21 Jun 2020 18:27:08: 5000000 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 18:27:12: 6000000 INFO @ Sun, 21 Jun 2020 18:27:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.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 18:27:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:17: 7000000 INFO @ Sun, 21 Jun 2020 18:27:18: 1000000 INFO @ Sun, 21 Jun 2020 18:27:23: 2000000 INFO @ Sun, 21 Jun 2020 18:27:23: 8000000 INFO @ Sun, 21 Jun 2020 18:27:27: 3000000 INFO @ Sun, 21 Jun 2020 18:27:28: 9000000 INFO @ Sun, 21 Jun 2020 18:27:31: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:31: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:31: #1 total tags in treatment: 9568257 INFO @ Sun, 21 Jun 2020 18:27:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:31: #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 18:27:31: #1 tags after filtering in treatment: 9568153 INFO @ Sun, 21 Jun 2020 18:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:31: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:32: #2 number of paired peaks: 2191 INFO @ Sun, 21 Jun 2020 18:27:32: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:32: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:32: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:32: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:32: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:27:32: #2 alternative fragment length(s) may be 3,80,591,594 bps INFO @ Sun, 21 Jun 2020 18:27:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.05_model.r WARNING @ Sun, 21 Jun 2020 18:27:32: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:32: #2 You may need to consider one of the other alternative d(s): 3,80,591,594 WARNING @ Sun, 21 Jun 2020 18:27:32: #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 18:27:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:32: 4000000 INFO @ Sun, 21 Jun 2020 18:27:37: 5000000 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 18:27:42: 6000000 INFO @ Sun, 21 Jun 2020 18:27:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.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 18:27:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:47: 7000000 INFO @ Sun, 21 Jun 2020 18:27:49: 1000000 INFO @ Sun, 21 Jun 2020 18:27:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:52: 8000000 INFO @ Sun, 21 Jun 2020 18:27:54: 2000000 INFO @ Sun, 21 Jun 2020 18:27:58: 9000000 INFO @ Sun, 21 Jun 2020 18:28:00: 3000000 INFO @ Sun, 21 Jun 2020 18:28:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:28:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:28:01: #1 total tags in treatment: 9568257 INFO @ Sun, 21 Jun 2020 18:28:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:01: #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 18:28:01: #1 tags after filtering in treatment: 9568153 INFO @ Sun, 21 Jun 2020 18:28:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:02: #2 number of paired peaks: 2191 INFO @ Sun, 21 Jun 2020 18:28:02: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:02: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:28:02: #2 alternative fragment length(s) may be 3,80,591,594 bps INFO @ Sun, 21 Jun 2020 18:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.10_model.r WARNING @ Sun, 21 Jun 2020 18:28:02: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:02: #2 You may need to consider one of the other alternative d(s): 3,80,591,594 WARNING @ Sun, 21 Jun 2020 18:28:02: #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 18:28:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.05_summits.bed INFO @ Sun, 21 Jun 2020 18:28:02: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (3377 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:06: 4000000 INFO @ Sun, 21 Jun 2020 18:28:11: 5000000 INFO @ Sun, 21 Jun 2020 18:28:17: 6000000 INFO @ Sun, 21 Jun 2020 18:28:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:28:22: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:28:28: 8000000 INFO @ Sun, 21 Jun 2020 18:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.10_summits.bed INFO @ Sun, 21 Jun 2020 18:28:32: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (2101 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:28:34: 9000000 INFO @ Sun, 21 Jun 2020 18:28:37: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:28:37: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:28:37: #1 total tags in treatment: 9568257 INFO @ Sun, 21 Jun 2020 18:28:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:28:37: #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 18:28:38: #1 tags after filtering in treatment: 9568153 INFO @ Sun, 21 Jun 2020 18:28:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:28:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:28:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:28:39: #2 number of paired peaks: 2191 INFO @ Sun, 21 Jun 2020 18:28:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:28:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:28:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:28:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:28:39: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 18:28:39: #2 alternative fragment length(s) may be 3,80,591,594 bps INFO @ Sun, 21 Jun 2020 18:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.20_model.r WARNING @ Sun, 21 Jun 2020 18:28:39: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:28:39: #2 You may need to consider one of the other alternative d(s): 3,80,591,594 WARNING @ Sun, 21 Jun 2020 18:28:39: #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 18:28:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:28:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:28:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:29:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:29:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:29:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055955/SRX2055955.20_summits.bed INFO @ Sun, 21 Jun 2020 18:29:08: Done! pass1 - making usageList (338 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 10 millis CompletedMACS2peakCalling