Job ID = 6456600 SRX = SRX367039 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:24:09 prefetch.2.10.7: 1) Downloading 'SRR1015601'... 2020-06-21T11:24:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:27:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:27:03 prefetch.2.10.7: 1) 'SRR1015601' was downloaded successfully Read 27999413 spots for SRR1015601/SRR1015601.sra Written 27999413 spots for SRR1015601/SRR1015601.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 27999413 reads; of these: 27999413 (100.00%) were unpaired; of these: 6696768 (23.92%) aligned 0 times 11278679 (40.28%) aligned exactly 1 time 10023966 (35.80%) aligned >1 times 76.08% 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] 12610964 / 21302645 = 0.5920 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 20:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.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 20:39:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:15: 1000000 INFO @ Sun, 21 Jun 2020 20:39:20: 2000000 INFO @ Sun, 21 Jun 2020 20:39:25: 3000000 INFO @ Sun, 21 Jun 2020 20:39:30: 4000000 INFO @ Sun, 21 Jun 2020 20:39:35: 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 20:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.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 20:39:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:40: 6000000 INFO @ Sun, 21 Jun 2020 20:39:44: 1000000 INFO @ Sun, 21 Jun 2020 20:39:46: 7000000 INFO @ Sun, 21 Jun 2020 20:39:49: 2000000 INFO @ Sun, 21 Jun 2020 20:39:51: 8000000 INFO @ Sun, 21 Jun 2020 20:39:54: 3000000 INFO @ Sun, 21 Jun 2020 20:39:55: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:39:55: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:39:55: #1 total tags in treatment: 8691681 INFO @ Sun, 21 Jun 2020 20:39:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:55: #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 20:39:56: #1 tags after filtering in treatment: 8691562 INFO @ Sun, 21 Jun 2020 20:39:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:56: #2 number of paired peaks: 2147 INFO @ Sun, 21 Jun 2020 20:39:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:56: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:56: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:56: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:56: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 20:39:56: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 20:39:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.05_model.r WARNING @ Sun, 21 Jun 2020 20:39:56: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:39:56: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 20:39:56: #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 20:39:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:58: 4000000 INFO @ Sun, 21 Jun 2020 20:40:03: 5000000 INFO @ Sun, 21 Jun 2020 20:40:07: 6000000 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 20:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.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 20:40:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:12: 7000000 INFO @ Sun, 21 Jun 2020 20:40:14: 1000000 INFO @ Sun, 21 Jun 2020 20:40:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:17: 8000000 INFO @ Sun, 21 Jun 2020 20:40:19: 2000000 INFO @ Sun, 21 Jun 2020 20:40:21: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:40:21: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:40:21: #1 total tags in treatment: 8691681 INFO @ Sun, 21 Jun 2020 20:40:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:21: #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 20:40:21: #1 tags after filtering in treatment: 8691562 INFO @ Sun, 21 Jun 2020 20:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:22: #2 number of paired peaks: 2147 INFO @ Sun, 21 Jun 2020 20:40:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:22: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 20:40:22: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 20:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.10_model.r WARNING @ Sun, 21 Jun 2020 20:40:22: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:22: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 20:40:22: #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 20:40:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:24: 3000000 INFO @ Sun, 21 Jun 2020 20:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.05_summits.bed INFO @ Sun, 21 Jun 2020 20:40:24: Done! pass1 - making usageList (748 chroms): 2 millis pass2 - checking and writing primary data (12131 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:28: 4000000 INFO @ Sun, 21 Jun 2020 20:40:33: 5000000 INFO @ Sun, 21 Jun 2020 20:40:38: 6000000 INFO @ Sun, 21 Jun 2020 20:40:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:42: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:47: 8000000 INFO @ Sun, 21 Jun 2020 20:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.10_summits.bed INFO @ Sun, 21 Jun 2020 20:40:48: Done! pass1 - making usageList (646 chroms): 1 millis pass2 - checking and writing primary data (5594 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:50: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 20:40:50: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 20:40:50: #1 total tags in treatment: 8691681 INFO @ Sun, 21 Jun 2020 20:40:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:50: #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 20:40:51: #1 tags after filtering in treatment: 8691562 INFO @ Sun, 21 Jun 2020 20:40:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:51: #2 number of paired peaks: 2147 INFO @ Sun, 21 Jun 2020 20:40:51: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:51: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:51: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:51: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:51: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 20:40:51: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sun, 21 Jun 2020 20:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.20_model.r WARNING @ Sun, 21 Jun 2020 20:40:51: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:51: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sun, 21 Jun 2020 20:40:51: #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 20:40:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:41:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX367039/SRX367039.20_summits.bed INFO @ Sun, 21 Jun 2020 20:41:18: Done! pass1 - making usageList (354 chroms): 1 millis pass2 - checking and writing primary data (1668 records, 4 fields): 11 millis CompletedMACS2peakCalling