Job ID = 6368005 SRX = SRX466468 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:59 prefetch.2.10.7: 1) Downloading 'SRR1163534'... 2020-06-15T23:44:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:06 prefetch.2.10.7: 'SRR1163534' is valid 2020-06-15T23:46:06 prefetch.2.10.7: 1) 'SRR1163534' was downloaded successfully Read 5595479 spots for SRR1163534/SRR1163534.sra Written 5595479 spots for SRR1163534/SRR1163534.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: 00:00:01 Multiseed full-index search: 00:01:22 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127540 (2.28%) aligned 0 times 4499900 (80.42%) aligned exactly 1 time 968039 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 319354 / 5467939 = 0.0584 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 @ Tue, 16 Jun 2020 08:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.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 @ Tue, 16 Jun 2020 08:49:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:39: 1000000 INFO @ Tue, 16 Jun 2020 08:49:45: 2000000 INFO @ Tue, 16 Jun 2020 08:49:51: 3000000 INFO @ Tue, 16 Jun 2020 08:49:58: 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 @ Tue, 16 Jun 2020 08:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.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 @ Tue, 16 Jun 2020 08:50:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:04: 5000000 INFO @ Tue, 16 Jun 2020 08:50:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:05: #1 total tags in treatment: 5148585 INFO @ Tue, 16 Jun 2020 08:50:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:50:05: #1 tags after filtering in treatment: 5148585 INFO @ Tue, 16 Jun 2020 08:50:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:05: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 08:50:05: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:05: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:50:05: #2 alternative fragment length(s) may be 3,48,583 bps INFO @ Tue, 16 Jun 2020 08:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:05: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:05: #2 You may need to consider one of the other alternative d(s): 3,48,583 WARNING @ Tue, 16 Jun 2020 08:50:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:50:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:09: 1000000 INFO @ Tue, 16 Jun 2020 08:50:15: 2000000 INFO @ Tue, 16 Jun 2020 08:50:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (544 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:22: 3000000 INFO @ Tue, 16 Jun 2020 08:50:28: 4000000 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 @ Tue, 16 Jun 2020 08:50:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.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 @ Tue, 16 Jun 2020 08:50:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:50:34: 5000000 INFO @ Tue, 16 Jun 2020 08:50:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:50:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:50:35: #1 total tags in treatment: 5148585 INFO @ Tue, 16 Jun 2020 08:50:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:50:35: #1 tags after filtering in treatment: 5148585 INFO @ Tue, 16 Jun 2020 08:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:35: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 08:50:35: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:35: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:50:35: #2 alternative fragment length(s) may be 3,48,583 bps INFO @ Tue, 16 Jun 2020 08:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:35: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:35: #2 You may need to consider one of the other alternative d(s): 3,48,583 WARNING @ Tue, 16 Jun 2020 08:50:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:50:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:39: 1000000 INFO @ Tue, 16 Jun 2020 08:50:44: 2000000 INFO @ Tue, 16 Jun 2020 08:50:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:49: 3000000 INFO @ Tue, 16 Jun 2020 08:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:55: 4000000 INFO @ Tue, 16 Jun 2020 08:51:00: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:51:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:00: #1 total tags in treatment: 5148585 INFO @ Tue, 16 Jun 2020 08:51:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:51:01: #1 tags after filtering in treatment: 5148585 INFO @ Tue, 16 Jun 2020 08:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:01: #2 number of paired peaks: 422 WARNING @ Tue, 16 Jun 2020 08:51:01: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:01: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:51:01: #2 alternative fragment length(s) may be 3,48,583 bps INFO @ Tue, 16 Jun 2020 08:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:01: #2 You may need to consider one of the other alternative d(s): 3,48,583 WARNING @ Tue, 16 Jun 2020 08:51:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:51:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466468/SRX466468.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (141 records, 4 fields): 1 millis CompletedMACS2peakCalling