Job ID = 6508014 SRX = SRX747305 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:07:56 prefetch.2.10.7: 1) Downloading 'SRR1635003'... 2020-06-26T14:07:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:08:59 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:09:00 prefetch.2.10.7: 'SRR1635003' is valid 2020-06-26T14:09:00 prefetch.2.10.7: 1) 'SRR1635003' was downloaded successfully 2020-06-26T14:09:32 prefetch.2.10.7: 'SRR1635003' has 6 unresolved dependencies 2020-06-26T14:09:32 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T14:09:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:09:49 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:09:49 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:09:49 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T14:09:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:10:06 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:10:06 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:10:06 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T14:10:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:10:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:10:23 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:10:23 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T14:10:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:10:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:10:39 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:10:39 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T14:10:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:10:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:10:56 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:10:56 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T14:10:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:11:12 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:11:12 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 21320771 spots for SRR1635003/SRR1635003.sra Written 21320771 spots for SRR1635003/SRR1635003.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: 00:02:21 21320771 reads; of these: 21320771 (100.00%) were unpaired; of these: 4230735 (19.84%) aligned 0 times 15225621 (71.41%) aligned exactly 1 time 1864415 (8.74%) aligned >1 times 80.16% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5491858 / 17090036 = 0.3213 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 23:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.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 23:18:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:18:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:18:06: 1000000 INFO @ Fri, 26 Jun 2020 23:18:11: 2000000 INFO @ Fri, 26 Jun 2020 23:18:16: 3000000 INFO @ Fri, 26 Jun 2020 23:18:22: 4000000 INFO @ Fri, 26 Jun 2020 23:18:27: 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 23:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.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 23:18:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:18:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:18:33: 6000000 INFO @ Fri, 26 Jun 2020 23:18:36: 1000000 INFO @ Fri, 26 Jun 2020 23:18:38: 7000000 INFO @ Fri, 26 Jun 2020 23:18:42: 2000000 INFO @ Fri, 26 Jun 2020 23:18:44: 8000000 INFO @ Fri, 26 Jun 2020 23:18:48: 3000000 INFO @ Fri, 26 Jun 2020 23:18:50: 9000000 INFO @ Fri, 26 Jun 2020 23:18:53: 4000000 INFO @ Fri, 26 Jun 2020 23:18:56: 10000000 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 23:18:59: 5000000 INFO @ Fri, 26 Jun 2020 23:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.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 23:19:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:19:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:19:02: 11000000 INFO @ Fri, 26 Jun 2020 23:19:05: 6000000 INFO @ Fri, 26 Jun 2020 23:19:05: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:19:05: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:19:05: #1 total tags in treatment: 11598178 INFO @ Fri, 26 Jun 2020 23:19:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:05: #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 23:19:06: #1 tags after filtering in treatment: 11598178 INFO @ Fri, 26 Jun 2020 23:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:19:06: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:19:07: 1000000 INFO @ Fri, 26 Jun 2020 23:19:07: #2 number of paired peaks: 565 WARNING @ Fri, 26 Jun 2020 23:19:07: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Fri, 26 Jun 2020 23:19:07: start model_add_line... INFO @ Fri, 26 Jun 2020 23:19:07: start X-correlation... INFO @ Fri, 26 Jun 2020 23:19:07: end of X-cor INFO @ Fri, 26 Jun 2020 23:19:07: #2 finished! INFO @ Fri, 26 Jun 2020 23:19:07: #2 predicted fragment length is 121 bps INFO @ Fri, 26 Jun 2020 23:19:07: #2 alternative fragment length(s) may be 121,588 bps INFO @ Fri, 26 Jun 2020 23:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.05_model.r INFO @ Fri, 26 Jun 2020 23:19:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:19:11: 7000000 INFO @ Fri, 26 Jun 2020 23:19:12: 2000000 INFO @ Fri, 26 Jun 2020 23:19:17: 8000000 INFO @ Fri, 26 Jun 2020 23:19:18: 3000000 INFO @ Fri, 26 Jun 2020 23:19:23: 9000000 INFO @ Fri, 26 Jun 2020 23:19:24: 4000000 INFO @ Fri, 26 Jun 2020 23:19:29: 10000000 INFO @ Fri, 26 Jun 2020 23:19:30: 5000000 INFO @ Fri, 26 Jun 2020 23:19:34: 11000000 INFO @ Fri, 26 Jun 2020 23:19:35: 6000000 INFO @ Fri, 26 Jun 2020 23:19:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:19:38: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:19:38: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:19:38: #1 total tags in treatment: 11598178 INFO @ Fri, 26 Jun 2020 23:19:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:38: #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 23:19:38: #1 tags after filtering in treatment: 11598178 INFO @ Fri, 26 Jun 2020 23:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:19:38: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:19:39: #2 number of paired peaks: 565 WARNING @ Fri, 26 Jun 2020 23:19:39: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Fri, 26 Jun 2020 23:19:39: start model_add_line... INFO @ Fri, 26 Jun 2020 23:19:39: start X-correlation... INFO @ Fri, 26 Jun 2020 23:19:39: end of X-cor INFO @ Fri, 26 Jun 2020 23:19:39: #2 finished! INFO @ Fri, 26 Jun 2020 23:19:39: #2 predicted fragment length is 121 bps INFO @ Fri, 26 Jun 2020 23:19:39: #2 alternative fragment length(s) may be 121,588 bps INFO @ Fri, 26 Jun 2020 23:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.10_model.r INFO @ Fri, 26 Jun 2020 23:19:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:19:41: 7000000 INFO @ Fri, 26 Jun 2020 23:19:46: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.05_summits.bed INFO @ Fri, 26 Jun 2020 23:19:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9499 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:19:51: 9000000 INFO @ Fri, 26 Jun 2020 23:19:56: 10000000 INFO @ Fri, 26 Jun 2020 23:20:02: 11000000 INFO @ Fri, 26 Jun 2020 23:20:05: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:20:05: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:20:05: #1 total tags in treatment: 11598178 INFO @ Fri, 26 Jun 2020 23:20:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:20:05: #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 23:20:05: #1 tags after filtering in treatment: 11598178 INFO @ Fri, 26 Jun 2020 23:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:20:05: #1 finished! INFO @ Fri, 26 Jun 2020 23:20:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:20:06: #2 number of paired peaks: 565 WARNING @ Fri, 26 Jun 2020 23:20:06: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Fri, 26 Jun 2020 23:20:06: start model_add_line... INFO @ Fri, 26 Jun 2020 23:20:06: start X-correlation... INFO @ Fri, 26 Jun 2020 23:20:06: end of X-cor INFO @ Fri, 26 Jun 2020 23:20:06: #2 finished! INFO @ Fri, 26 Jun 2020 23:20:06: #2 predicted fragment length is 121 bps INFO @ Fri, 26 Jun 2020 23:20:06: #2 alternative fragment length(s) may be 121,588 bps INFO @ Fri, 26 Jun 2020 23:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.20_model.r INFO @ Fri, 26 Jun 2020 23:20:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:20:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:20:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.10_summits.bed INFO @ Fri, 26 Jun 2020 23:20:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4649 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:20:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747305/SRX747305.20_summits.bed INFO @ Fri, 26 Jun 2020 23:20:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1494 records, 4 fields): 3 millis CompletedMACS2peakCalling