Job ID = 6507879 SRX = SRX494964 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:18:03 prefetch.2.10.7: 1) Downloading 'SRR1198496'... 2020-06-26T13:18:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:18:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:18:48 prefetch.2.10.7: 'SRR1198496' is valid 2020-06-26T13:18:48 prefetch.2.10.7: 1) 'SRR1198496' was downloaded successfully Read 6065387 spots for SRR1198496/SRR1198496.sra Written 6065387 spots for SRR1198496/SRR1198496.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: 00:01:04 6065387 reads; of these: 6065387 (100.00%) were unpaired; of these: 2530818 (41.73%) aligned 0 times 3025321 (49.88%) aligned exactly 1 time 509248 (8.40%) aligned >1 times 58.27% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2636701 / 3534569 = 0.7460 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 22:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.bam'] # control file = None # effective genome size = 9.00e+07 # 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 22:21:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:21:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:21:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:21:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:21:20: #1 total tags in treatment: 897868 INFO @ Fri, 26 Jun 2020 22:21:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:21:20: #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 22:21:20: #1 tags after filtering in treatment: 897868 INFO @ Fri, 26 Jun 2020 22:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:21:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:21:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:21:20: #2 number of paired peaks: 2533 INFO @ Fri, 26 Jun 2020 22:21:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:21:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:21:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:21:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:21:20: #2 predicted fragment length is 95 bps INFO @ Fri, 26 Jun 2020 22:21:20: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 26 Jun 2020 22:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.05_model.r WARNING @ Fri, 26 Jun 2020 22:21:20: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:21:20: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Fri, 26 Jun 2020 22:21:20: #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 22:21:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:21:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.05_summits.bed INFO @ Fri, 26 Jun 2020 22:21:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2408 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 22:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.bam'] # control file = None # effective genome size = 9.00e+07 # 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 22:21:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:21:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:21:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:21:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:21:49: #1 total tags in treatment: 897868 INFO @ Fri, 26 Jun 2020 22:21:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:21:49: #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 22:21:49: #1 tags after filtering in treatment: 897868 INFO @ Fri, 26 Jun 2020 22:21:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:21:49: #1 finished! INFO @ Fri, 26 Jun 2020 22:21:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:21:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:21:49: #2 number of paired peaks: 2533 INFO @ Fri, 26 Jun 2020 22:21:49: start model_add_line... INFO @ Fri, 26 Jun 2020 22:21:49: start X-correlation... INFO @ Fri, 26 Jun 2020 22:21:49: end of X-cor INFO @ Fri, 26 Jun 2020 22:21:49: #2 finished! INFO @ Fri, 26 Jun 2020 22:21:49: #2 predicted fragment length is 95 bps INFO @ Fri, 26 Jun 2020 22:21:49: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 26 Jun 2020 22:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.10_model.r WARNING @ Fri, 26 Jun 2020 22:21:49: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:21:49: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Fri, 26 Jun 2020 22:21:49: #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 22:21:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:21:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:21:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:21:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:21:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.10_summits.bed INFO @ Fri, 26 Jun 2020 22:21:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 22:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.bam'] # control file = None # effective genome size = 9.00e+07 # 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 22:22:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:22:13: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:22:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:22:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:22:19: #1 total tags in treatment: 897868 INFO @ Fri, 26 Jun 2020 22:22:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:22:19: #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 22:22:19: #1 tags after filtering in treatment: 897868 INFO @ Fri, 26 Jun 2020 22:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:22:19: #1 finished! INFO @ Fri, 26 Jun 2020 22:22:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:22:19: #2 number of paired peaks: 2533 INFO @ Fri, 26 Jun 2020 22:22:19: start model_add_line... INFO @ Fri, 26 Jun 2020 22:22:19: start X-correlation... INFO @ Fri, 26 Jun 2020 22:22:19: end of X-cor INFO @ Fri, 26 Jun 2020 22:22:19: #2 finished! INFO @ Fri, 26 Jun 2020 22:22:19: #2 predicted fragment length is 95 bps INFO @ Fri, 26 Jun 2020 22:22:19: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 26 Jun 2020 22:22:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.20_model.r WARNING @ Fri, 26 Jun 2020 22:22:19: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:22:19: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Fri, 26 Jun 2020 22:22:19: #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 22:22:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:22:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:22:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494964/SRX494964.20_summits.bed INFO @ Fri, 26 Jun 2020 22:22:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (566 records, 4 fields): 2 millis CompletedMACS2peakCalling