Job ID = 6508004 SRX = SRX747297 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:37:48 prefetch.2.10.7: 1) Downloading 'SRR1634995'... 2020-06-26T13:37:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:38:29 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:38:29 prefetch.2.10.7: 'SRR1634995' is valid 2020-06-26T13:38:29 prefetch.2.10.7: 1) 'SRR1634995' was downloaded successfully 2020-06-26T13:39:02 prefetch.2.10.7: 'SRR1634995' has 6 unresolved dependencies 2020-06-26T13:39:02 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T13:39:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:39:18 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:39:18 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:39:18 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T13:39:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:39:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:39:34 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:39:34 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T13:39:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:39:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:39:50 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:39:50 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T13:39:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:40:06 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:40:06 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:40:06 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T13:40:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:40:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:40:23 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:40:23 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T13:40:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:40:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:40:39 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 11035931 spots for SRR1634995/SRR1634995.sra Written 11035931 spots for SRR1634995/SRR1634995.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: 00:01:44 11035931 reads; of these: 11035931 (100.00%) were unpaired; of these: 1133980 (10.28%) aligned 0 times 8248431 (74.74%) aligned exactly 1 time 1653520 (14.98%) aligned >1 times 89.72% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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] 1255396 / 9901951 = 0.1268 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 22:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.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 22:45:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:23: 1000000 INFO @ Fri, 26 Jun 2020 22:45:29: 2000000 INFO @ Fri, 26 Jun 2020 22:45:34: 3000000 INFO @ Fri, 26 Jun 2020 22:45:40: 4000000 INFO @ Fri, 26 Jun 2020 22:45:45: 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 @ Fri, 26 Jun 2020 22:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.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 22:45:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:45:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:45:51: 6000000 INFO @ Fri, 26 Jun 2020 22:45:54: 1000000 INFO @ Fri, 26 Jun 2020 22:45:56: 7000000 INFO @ Fri, 26 Jun 2020 22:46:00: 2000000 INFO @ Fri, 26 Jun 2020 22:46:02: 8000000 INFO @ Fri, 26 Jun 2020 22:46:06: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:46:06: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:46:06: #1 total tags in treatment: 8646555 INFO @ Fri, 26 Jun 2020 22:46:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:46:06: #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 22:46:06: #1 tags after filtering in treatment: 8646555 INFO @ Fri, 26 Jun 2020 22:46:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:46:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:46:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:46:07: 3000000 INFO @ Fri, 26 Jun 2020 22:46:07: #2 number of paired peaks: 325 WARNING @ Fri, 26 Jun 2020 22:46:07: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 26 Jun 2020 22:46:07: start model_add_line... INFO @ Fri, 26 Jun 2020 22:46:07: start X-correlation... INFO @ Fri, 26 Jun 2020 22:46:07: end of X-cor INFO @ Fri, 26 Jun 2020 22:46:07: #2 finished! INFO @ Fri, 26 Jun 2020 22:46:07: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 22:46:07: #2 alternative fragment length(s) may be 3,34,508,512 bps INFO @ Fri, 26 Jun 2020 22:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.05_model.r WARNING @ Fri, 26 Jun 2020 22:46:07: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:46:07: #2 You may need to consider one of the other alternative d(s): 3,34,508,512 WARNING @ Fri, 26 Jun 2020 22:46:07: #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 22:46:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:46:12: 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 @ Fri, 26 Jun 2020 22:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.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 22:46:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:46:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:46:18: 5000000 INFO @ Fri, 26 Jun 2020 22:46:24: 1000000 INFO @ Fri, 26 Jun 2020 22:46:25: 6000000 INFO @ Fri, 26 Jun 2020 22:46:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:46:30: 2000000 INFO @ Fri, 26 Jun 2020 22:46:31: 7000000 INFO @ Fri, 26 Jun 2020 22:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.05_summits.bed INFO @ Fri, 26 Jun 2020 22:46:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (636 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:46:35: 3000000 INFO @ Fri, 26 Jun 2020 22:46:37: 8000000 INFO @ Fri, 26 Jun 2020 22:46:41: 4000000 INFO @ Fri, 26 Jun 2020 22:46:41: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:46:41: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:46:41: #1 total tags in treatment: 8646555 INFO @ Fri, 26 Jun 2020 22:46:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:46:41: #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 22:46:41: #1 tags after filtering in treatment: 8646555 INFO @ Fri, 26 Jun 2020 22:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:46:41: #1 finished! INFO @ Fri, 26 Jun 2020 22:46:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:46:42: #2 number of paired peaks: 325 WARNING @ Fri, 26 Jun 2020 22:46:42: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 26 Jun 2020 22:46:42: start model_add_line... INFO @ Fri, 26 Jun 2020 22:46:42: start X-correlation... INFO @ Fri, 26 Jun 2020 22:46:42: end of X-cor INFO @ Fri, 26 Jun 2020 22:46:42: #2 finished! INFO @ Fri, 26 Jun 2020 22:46:42: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 22:46:42: #2 alternative fragment length(s) may be 3,34,508,512 bps INFO @ Fri, 26 Jun 2020 22:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.10_model.r WARNING @ Fri, 26 Jun 2020 22:46:42: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:46:42: #2 You may need to consider one of the other alternative d(s): 3,34,508,512 WARNING @ Fri, 26 Jun 2020 22:46:42: #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 22:46:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:46:46: 5000000 INFO @ Fri, 26 Jun 2020 22:46:52: 6000000 INFO @ Fri, 26 Jun 2020 22:46:57: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:47:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:47:03: 8000000 INFO @ Fri, 26 Jun 2020 22:47:06: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:47:06: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:47:06: #1 total tags in treatment: 8646555 INFO @ Fri, 26 Jun 2020 22:47:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:47:06: #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 22:47:06: #1 tags after filtering in treatment: 8646555 INFO @ Fri, 26 Jun 2020 22:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:47:06: #1 finished! INFO @ Fri, 26 Jun 2020 22:47:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:47:07: #2 number of paired peaks: 325 WARNING @ Fri, 26 Jun 2020 22:47:07: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Fri, 26 Jun 2020 22:47:07: start model_add_line... INFO @ Fri, 26 Jun 2020 22:47:07: start X-correlation... INFO @ Fri, 26 Jun 2020 22:47:07: end of X-cor INFO @ Fri, 26 Jun 2020 22:47:07: #2 finished! INFO @ Fri, 26 Jun 2020 22:47:07: #2 predicted fragment length is 34 bps INFO @ Fri, 26 Jun 2020 22:47:07: #2 alternative fragment length(s) may be 3,34,508,512 bps INFO @ Fri, 26 Jun 2020 22:47:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.20_model.r WARNING @ Fri, 26 Jun 2020 22:47:07: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:47:07: #2 You may need to consider one of the other alternative d(s): 3,34,508,512 WARNING @ Fri, 26 Jun 2020 22:47:07: #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 22:47:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.10_summits.bed INFO @ Fri, 26 Jun 2020 22:47:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:47:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747297/SRX747297.20_summits.bed INFO @ Fri, 26 Jun 2020 22:47:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (90 records, 4 fields): 1 millis CompletedMACS2peakCalling