Job ID = 6508005 SRX = SRX747298 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:17:11 prefetch.2.10.7: 1) Downloading 'SRR1634996'... 2020-06-26T14:17:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:18:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:18:34 prefetch.2.10.7: 'SRR1634996' is valid 2020-06-26T14:18:34 prefetch.2.10.7: 1) 'SRR1634996' was downloaded successfully 2020-06-26T14:19:07 prefetch.2.10.7: 'SRR1634996' has 6 unresolved dependencies 2020-06-26T14:19:07 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T14:19:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:19:23 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:19:23 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:19:23 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T14:19:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:19:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:19:39 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:19:39 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T14:19:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:19:57 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:19:57 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:19:57 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T14:19:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:20:13 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:20:13 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:20:13 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T14:20:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:20:28 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:20:28 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T14:20:28 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T14:20:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:20:45 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:20:45 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 14616230 spots for SRR1634996/SRR1634996.sra Written 14616230 spots for SRR1634996/SRR1634996.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: 00:02:08 14616230 reads; of these: 14616230 (100.00%) were unpaired; of these: 1661575 (11.37%) aligned 0 times 10841095 (74.17%) aligned exactly 1 time 2113560 (14.46%) aligned >1 times 88.63% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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] 1922182 / 12954655 = 0.1484 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 23:26:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.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 23:26:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:26:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:26:45: 1000000 INFO @ Fri, 26 Jun 2020 23:26:51: 2000000 INFO @ Fri, 26 Jun 2020 23:26:58: 3000000 INFO @ Fri, 26 Jun 2020 23:27:04: 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 @ Fri, 26 Jun 2020 23:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.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 23:27:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:27:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:27:10: 5000000 INFO @ Fri, 26 Jun 2020 23:27:16: 1000000 INFO @ Fri, 26 Jun 2020 23:27:17: 6000000 INFO @ Fri, 26 Jun 2020 23:27:22: 2000000 INFO @ Fri, 26 Jun 2020 23:27:23: 7000000 INFO @ Fri, 26 Jun 2020 23:27:28: 3000000 INFO @ Fri, 26 Jun 2020 23:27:30: 8000000 INFO @ Fri, 26 Jun 2020 23:27:35: 4000000 INFO @ Fri, 26 Jun 2020 23:27:36: 9000000 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 23:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.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 23:27:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:27:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:27:41: 5000000 INFO @ Fri, 26 Jun 2020 23:27:42: 10000000 INFO @ Fri, 26 Jun 2020 23:27:46: 1000000 INFO @ Fri, 26 Jun 2020 23:27:47: 6000000 INFO @ Fri, 26 Jun 2020 23:27:49: 11000000 INFO @ Fri, 26 Jun 2020 23:27:49: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:27:49: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:27:49: #1 total tags in treatment: 11032473 INFO @ Fri, 26 Jun 2020 23:27:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:27:49: #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 23:27:49: #1 tags after filtering in treatment: 11032473 INFO @ Fri, 26 Jun 2020 23:27:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:27:49: #1 finished! INFO @ Fri, 26 Jun 2020 23:27:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:27:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:27:50: #2 number of paired peaks: 284 WARNING @ Fri, 26 Jun 2020 23:27:50: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 26 Jun 2020 23:27:50: start model_add_line... INFO @ Fri, 26 Jun 2020 23:27:50: start X-correlation... INFO @ Fri, 26 Jun 2020 23:27:50: end of X-cor INFO @ Fri, 26 Jun 2020 23:27:50: #2 finished! INFO @ Fri, 26 Jun 2020 23:27:50: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 23:27:50: #2 alternative fragment length(s) may be 2,35,581 bps INFO @ Fri, 26 Jun 2020 23:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.05_model.r WARNING @ Fri, 26 Jun 2020 23:27:50: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:27:50: #2 You may need to consider one of the other alternative d(s): 2,35,581 WARNING @ Fri, 26 Jun 2020 23:27:50: #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 23:27:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:27:53: 2000000 INFO @ Fri, 26 Jun 2020 23:27:54: 7000000 INFO @ Fri, 26 Jun 2020 23:28:00: 8000000 INFO @ Fri, 26 Jun 2020 23:28:00: 3000000 INFO @ Fri, 26 Jun 2020 23:28:06: 9000000 INFO @ Fri, 26 Jun 2020 23:28:08: 4000000 INFO @ Fri, 26 Jun 2020 23:28:13: 10000000 INFO @ Fri, 26 Jun 2020 23:28:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:28:14: 5000000 INFO @ Fri, 26 Jun 2020 23:28:19: 11000000 INFO @ Fri, 26 Jun 2020 23:28:19: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:28:19: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:28:19: #1 total tags in treatment: 11032473 INFO @ Fri, 26 Jun 2020 23:28:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:28:19: #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 23:28:19: #1 tags after filtering in treatment: 11032473 INFO @ Fri, 26 Jun 2020 23:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:28:19: #1 finished! INFO @ Fri, 26 Jun 2020 23:28:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:28:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:28:20: #2 number of paired peaks: 284 WARNING @ Fri, 26 Jun 2020 23:28:20: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 26 Jun 2020 23:28:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:28:20: start X-correlation... INFO @ Fri, 26 Jun 2020 23:28:20: end of X-cor INFO @ Fri, 26 Jun 2020 23:28:20: #2 finished! INFO @ Fri, 26 Jun 2020 23:28:20: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 23:28:20: #2 alternative fragment length(s) may be 2,35,581 bps INFO @ Fri, 26 Jun 2020 23:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.10_model.r WARNING @ Fri, 26 Jun 2020 23:28:20: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:28:20: #2 You may need to consider one of the other alternative d(s): 2,35,581 WARNING @ Fri, 26 Jun 2020 23:28:20: #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 23:28:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:28:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:28:21: 6000000 INFO @ Fri, 26 Jun 2020 23:28:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:28:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:28:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.05_summits.bed INFO @ Fri, 26 Jun 2020 23:28:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (757 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:28:28: 7000000 INFO @ Fri, 26 Jun 2020 23:28:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:28:41: 9000000 INFO @ Fri, 26 Jun 2020 23:28:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:28:47: 10000000 INFO @ Fri, 26 Jun 2020 23:28:54: 11000000 INFO @ Fri, 26 Jun 2020 23:28:54: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:28:54: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:28:54: #1 total tags in treatment: 11032473 INFO @ Fri, 26 Jun 2020 23:28:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:28:54: #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 23:28:54: #1 tags after filtering in treatment: 11032473 INFO @ Fri, 26 Jun 2020 23:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:28:54: #1 finished! INFO @ Fri, 26 Jun 2020 23:28:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:28:55: #2 number of paired peaks: 284 WARNING @ Fri, 26 Jun 2020 23:28:55: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Fri, 26 Jun 2020 23:28:55: start model_add_line... INFO @ Fri, 26 Jun 2020 23:28:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:28:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:28:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.10_summits.bed INFO @ Fri, 26 Jun 2020 23:28:55: Done! INFO @ Fri, 26 Jun 2020 23:28:55: start X-correlation... INFO @ Fri, 26 Jun 2020 23:28:55: end of X-cor INFO @ Fri, 26 Jun 2020 23:28:55: #2 finished! INFO @ Fri, 26 Jun 2020 23:28:55: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 23:28:55: #2 alternative fragment length(s) may be 2,35,581 bps INFO @ Fri, 26 Jun 2020 23:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.20_model.r WARNING @ Fri, 26 Jun 2020 23:28:55: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:28:55: #2 You may need to consider one of the other alternative d(s): 2,35,581 WARNING @ Fri, 26 Jun 2020 23:28:55: #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 23:28:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:28:55: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (337 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:29:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747298/SRX747298.20_summits.bed INFO @ Fri, 26 Jun 2020 23:29:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling