Job ID = 6508012 SRX = SRX747303 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:50:57 prefetch.2.10.7: 1) Downloading 'SRR1635001'... 2020-06-26T13:50:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:51:42 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:51:42 prefetch.2.10.7: 'SRR1635001' is valid 2020-06-26T13:51:42 prefetch.2.10.7: 1) 'SRR1635001' was downloaded successfully 2020-06-26T13:52:15 prefetch.2.10.7: 'SRR1635001' has 6 unresolved dependencies 2020-06-26T13:52:15 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T13:52:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:52:30 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:52:30 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:52:30 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T13:52:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:52:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:52:46 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:52:46 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T13:52:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:53:01 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:53:01 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:53:01 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T13:53:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:53:18 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:53:18 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:53:18 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T13:53:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:53:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:53:36 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:53:36 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T13:53:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:53:52 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:53:52 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 27367092 spots for SRR1635001/SRR1635001.sra Written 27367092 spots for SRR1635001/SRR1635001.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: 00:03:58 27367092 reads; of these: 27367092 (100.00%) were unpaired; of these: 1033713 (3.78%) aligned 0 times 21384032 (78.14%) aligned exactly 1 time 4949347 (18.09%) aligned >1 times 96.22% overall alignment rate Time searching: 00:03:58 Overall time: 00:03:58 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] 4806213 / 26333379 = 0.1825 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 23:03:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.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 23:03:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:03:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:03:28: 1000000 INFO @ Fri, 26 Jun 2020 23:03:33: 2000000 INFO @ Fri, 26 Jun 2020 23:03:37: 3000000 INFO @ Fri, 26 Jun 2020 23:03:42: 4000000 INFO @ Fri, 26 Jun 2020 23:03:46: 5000000 INFO @ Fri, 26 Jun 2020 23:03:51: 6000000 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 23:03:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.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 23:03:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:03:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:03:55: 7000000 INFO @ Fri, 26 Jun 2020 23:03:59: 1000000 INFO @ Fri, 26 Jun 2020 23:04:00: 8000000 INFO @ Fri, 26 Jun 2020 23:04:03: 2000000 INFO @ Fri, 26 Jun 2020 23:04:04: 9000000 INFO @ Fri, 26 Jun 2020 23:04:08: 3000000 INFO @ Fri, 26 Jun 2020 23:04:09: 10000000 INFO @ Fri, 26 Jun 2020 23:04:13: 4000000 INFO @ Fri, 26 Jun 2020 23:04:14: 11000000 INFO @ Fri, 26 Jun 2020 23:04:17: 5000000 INFO @ Fri, 26 Jun 2020 23:04:18: 12000000 INFO @ Fri, 26 Jun 2020 23:04:22: 6000000 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 23:04:23: 13000000 INFO @ Fri, 26 Jun 2020 23:04:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.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 23:04:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:04:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:04:27: 7000000 INFO @ Fri, 26 Jun 2020 23:04:28: 14000000 INFO @ Fri, 26 Jun 2020 23:04:29: 1000000 INFO @ Fri, 26 Jun 2020 23:04:32: 8000000 INFO @ Fri, 26 Jun 2020 23:04:33: 15000000 INFO @ Fri, 26 Jun 2020 23:04:35: 2000000 INFO @ Fri, 26 Jun 2020 23:04:37: 9000000 INFO @ Fri, 26 Jun 2020 23:04:38: 16000000 INFO @ Fri, 26 Jun 2020 23:04:40: 3000000 INFO @ Fri, 26 Jun 2020 23:04:41: 10000000 INFO @ Fri, 26 Jun 2020 23:04:42: 17000000 INFO @ Fri, 26 Jun 2020 23:04:45: 4000000 INFO @ Fri, 26 Jun 2020 23:04:46: 11000000 INFO @ Fri, 26 Jun 2020 23:04:47: 18000000 INFO @ Fri, 26 Jun 2020 23:04:51: 5000000 INFO @ Fri, 26 Jun 2020 23:04:51: 12000000 INFO @ Fri, 26 Jun 2020 23:04:52: 19000000 INFO @ Fri, 26 Jun 2020 23:04:56: 6000000 INFO @ Fri, 26 Jun 2020 23:04:56: 13000000 INFO @ Fri, 26 Jun 2020 23:04:57: 20000000 INFO @ Fri, 26 Jun 2020 23:05:01: 14000000 INFO @ Fri, 26 Jun 2020 23:05:01: 7000000 INFO @ Fri, 26 Jun 2020 23:05:02: 21000000 INFO @ Fri, 26 Jun 2020 23:05:04: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:05:04: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:05:04: #1 total tags in treatment: 21527166 INFO @ Fri, 26 Jun 2020 23:05:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:05:04: #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 23:05:05: #1 tags after filtering in treatment: 21527166 INFO @ Fri, 26 Jun 2020 23:05:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:05:05: #1 finished! INFO @ Fri, 26 Jun 2020 23:05:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:05:06: 15000000 INFO @ Fri, 26 Jun 2020 23:05:06: #2 number of paired peaks: 251 WARNING @ Fri, 26 Jun 2020 23:05:06: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 26 Jun 2020 23:05:06: start model_add_line... INFO @ Fri, 26 Jun 2020 23:05:06: 8000000 INFO @ Fri, 26 Jun 2020 23:05:06: start X-correlation... INFO @ Fri, 26 Jun 2020 23:05:06: end of X-cor INFO @ Fri, 26 Jun 2020 23:05:06: #2 finished! INFO @ Fri, 26 Jun 2020 23:05:06: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:05:06: #2 alternative fragment length(s) may be 1,29,565 bps INFO @ Fri, 26 Jun 2020 23:05:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.05_model.r WARNING @ Fri, 26 Jun 2020 23:05:06: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:05:06: #2 You may need to consider one of the other alternative d(s): 1,29,565 WARNING @ Fri, 26 Jun 2020 23:05:06: #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 23:05:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:05:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:05:11: 16000000 INFO @ Fri, 26 Jun 2020 23:05:12: 9000000 INFO @ Fri, 26 Jun 2020 23:05:15: 17000000 INFO @ Fri, 26 Jun 2020 23:05:17: 10000000 INFO @ Fri, 26 Jun 2020 23:05:20: 18000000 INFO @ Fri, 26 Jun 2020 23:05:22: 11000000 INFO @ Fri, 26 Jun 2020 23:05:25: 19000000 INFO @ Fri, 26 Jun 2020 23:05:27: 12000000 INFO @ Fri, 26 Jun 2020 23:05:30: 20000000 INFO @ Fri, 26 Jun 2020 23:05:32: 13000000 INFO @ Fri, 26 Jun 2020 23:05:35: 21000000 INFO @ Fri, 26 Jun 2020 23:05:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:05:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:05:37: #1 total tags in treatment: 21527166 INFO @ Fri, 26 Jun 2020 23:05:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:05:37: #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 23:05:37: 14000000 INFO @ Fri, 26 Jun 2020 23:05:38: #1 tags after filtering in treatment: 21527166 INFO @ Fri, 26 Jun 2020 23:05:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:05:38: #1 finished! INFO @ Fri, 26 Jun 2020 23:05:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:05:39: #2 number of paired peaks: 251 WARNING @ Fri, 26 Jun 2020 23:05:39: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 26 Jun 2020 23:05:39: start model_add_line... INFO @ Fri, 26 Jun 2020 23:05:39: start X-correlation... INFO @ Fri, 26 Jun 2020 23:05:39: end of X-cor INFO @ Fri, 26 Jun 2020 23:05:39: #2 finished! INFO @ Fri, 26 Jun 2020 23:05:39: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:05:39: #2 alternative fragment length(s) may be 1,29,565 bps INFO @ Fri, 26 Jun 2020 23:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.10_model.r WARNING @ Fri, 26 Jun 2020 23:05:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:05:39: #2 You may need to consider one of the other alternative d(s): 1,29,565 WARNING @ Fri, 26 Jun 2020 23:05:39: #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 23:05:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:05:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:05:42: 15000000 INFO @ Fri, 26 Jun 2020 23:05:47: 16000000 INFO @ Fri, 26 Jun 2020 23:05:52: 17000000 INFO @ Fri, 26 Jun 2020 23:05:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.05_summits.bed INFO @ Fri, 26 Jun 2020 23:05:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:05:57: 18000000 INFO @ Fri, 26 Jun 2020 23:06:02: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:06:07: 20000000 INFO @ Fri, 26 Jun 2020 23:06:12: 21000000 INFO @ Fri, 26 Jun 2020 23:06:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:06:15: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 23:06:15: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 23:06:15: #1 total tags in treatment: 21527166 INFO @ Fri, 26 Jun 2020 23:06:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:06:15: #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 23:06:15: #1 tags after filtering in treatment: 21527166 INFO @ Fri, 26 Jun 2020 23:06:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:06:15: #1 finished! INFO @ Fri, 26 Jun 2020 23:06:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:06:17: #2 number of paired peaks: 251 WARNING @ Fri, 26 Jun 2020 23:06:17: Fewer paired peaks (251) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 251 pairs to build model! INFO @ Fri, 26 Jun 2020 23:06:17: start model_add_line... INFO @ Fri, 26 Jun 2020 23:06:17: start X-correlation... INFO @ Fri, 26 Jun 2020 23:06:17: end of X-cor INFO @ Fri, 26 Jun 2020 23:06:17: #2 finished! INFO @ Fri, 26 Jun 2020 23:06:17: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:06:17: #2 alternative fragment length(s) may be 1,29,565 bps INFO @ Fri, 26 Jun 2020 23:06:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.20_model.r WARNING @ Fri, 26 Jun 2020 23:06:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:06:17: #2 You may need to consider one of the other alternative d(s): 1,29,565 WARNING @ Fri, 26 Jun 2020 23:06:17: #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 23:06:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:06:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:06:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:06:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:06:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.10_summits.bed INFO @ Fri, 26 Jun 2020 23:06:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:06:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:07:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:07:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:07:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747303/SRX747303.20_summits.bed INFO @ Fri, 26 Jun 2020 23:07:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling