Job ID = 6498599 SRX = SRX645108 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:59:19 prefetch.2.10.7: 1) Downloading 'SRR1505707'... 2020-06-25T23:59:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:08:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:08:35 prefetch.2.10.7: 1) 'SRR1505707' was downloaded successfully Read 40000000 spots for SRR1505707/SRR1505707.sra Written 40000000 spots for SRR1505707/SRR1505707.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: 00:15:26 40000000 reads; of these: 40000000 (100.00%) were unpaired; of these: 28605444 (71.51%) aligned 0 times 8347632 (20.87%) aligned exactly 1 time 3046924 (7.62%) aligned >1 times 28.49% overall alignment rate Time searching: 00:15:26 Overall time: 00:15:26 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 8701196 / 11394556 = 0.7636 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 @ Fri, 26 Jun 2020 09:30:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.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 @ Fri, 26 Jun 2020 09:30:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:30:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:30:40: 1000000 INFO @ Fri, 26 Jun 2020 09:30:49: 2000000 INFO @ Fri, 26 Jun 2020 09:30:55: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:30:55: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:30:55: #1 total tags in treatment: 2693360 INFO @ Fri, 26 Jun 2020 09:30:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:30:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:30:55: #1 tags after filtering in treatment: 2693360 INFO @ Fri, 26 Jun 2020 09:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:30:55: #1 finished! INFO @ Fri, 26 Jun 2020 09:30:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:30:55: #2 number of paired peaks: 1989 INFO @ Fri, 26 Jun 2020 09:30:55: start model_add_line... INFO @ Fri, 26 Jun 2020 09:30:55: start X-correlation... INFO @ Fri, 26 Jun 2020 09:30:55: end of X-cor INFO @ Fri, 26 Jun 2020 09:30:55: #2 finished! INFO @ Fri, 26 Jun 2020 09:30:55: #2 predicted fragment length is 89 bps INFO @ Fri, 26 Jun 2020 09:30:55: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 26 Jun 2020 09:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.05_model.r WARNING @ Fri, 26 Jun 2020 09:30:55: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:30:55: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Fri, 26 Jun 2020 09:30:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:30:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:30:55: #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 @ Fri, 26 Jun 2020 09:31:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.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 @ Fri, 26 Jun 2020 09:31:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:31:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:31:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.05_summits.bed INFO @ Fri, 26 Jun 2020 09:31:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3458 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:31:10: 1000000 INFO @ Fri, 26 Jun 2020 09:31:18: 2000000 INFO @ Fri, 26 Jun 2020 09:31:24: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:31:24: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:31:24: #1 total tags in treatment: 2693360 INFO @ Fri, 26 Jun 2020 09:31:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:31:24: #1 tags after filtering in treatment: 2693360 INFO @ Fri, 26 Jun 2020 09:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:31:24: #1 finished! INFO @ Fri, 26 Jun 2020 09:31:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:31:24: #2 number of paired peaks: 1989 INFO @ Fri, 26 Jun 2020 09:31:24: start model_add_line... INFO @ Fri, 26 Jun 2020 09:31:24: start X-correlation... INFO @ Fri, 26 Jun 2020 09:31:24: end of X-cor INFO @ Fri, 26 Jun 2020 09:31:24: #2 finished! INFO @ Fri, 26 Jun 2020 09:31:24: #2 predicted fragment length is 89 bps INFO @ Fri, 26 Jun 2020 09:31:24: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 26 Jun 2020 09:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.10_model.r WARNING @ Fri, 26 Jun 2020 09:31:24: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:31:24: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Fri, 26 Jun 2020 09:31:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:31:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:31:24: #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 @ Fri, 26 Jun 2020 09:31:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.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 @ Fri, 26 Jun 2020 09:31:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:31:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.10_summits.bed INFO @ Fri, 26 Jun 2020 09:31:35: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1574 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:31:43: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:31:54: 2000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:32:01: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:32:01: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:32:01: #1 total tags in treatment: 2693360 INFO @ Fri, 26 Jun 2020 09:32:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:32:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:32:01: #1 tags after filtering in treatment: 2693360 INFO @ Fri, 26 Jun 2020 09:32:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:32:01: #1 finished! INFO @ Fri, 26 Jun 2020 09:32:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:32:02: #2 number of paired peaks: 1989 INFO @ Fri, 26 Jun 2020 09:32:02: start model_add_line... INFO @ Fri, 26 Jun 2020 09:32:02: start X-correlation... INFO @ Fri, 26 Jun 2020 09:32:02: end of X-cor INFO @ Fri, 26 Jun 2020 09:32:02: #2 finished! INFO @ Fri, 26 Jun 2020 09:32:02: #2 predicted fragment length is 89 bps INFO @ Fri, 26 Jun 2020 09:32:02: #2 alternative fragment length(s) may be 89 bps INFO @ Fri, 26 Jun 2020 09:32:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.20_model.r WARNING @ Fri, 26 Jun 2020 09:32:02: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:32:02: #2 You may need to consider one of the other alternative d(s): 89 WARNING @ Fri, 26 Jun 2020 09:32:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:32:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:32:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:32:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:32:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:32:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:32:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645108/SRX645108.20_summits.bed INFO @ Fri, 26 Jun 2020 09:32:13: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 2 millis CompletedMACS2peakCalling