Job ID = 6366883 SRX = SRX2543051 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:23 prefetch.2.10.7: 1) Downloading 'SRR5235987'... 2020-06-15T23:06:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:37 prefetch.2.10.7: 'SRR5235987' is valid 2020-06-15T23:07:37 prefetch.2.10.7: 1) 'SRR5235987' was downloaded successfully 2020-06-15T23:07:37 prefetch.2.10.7: 'SRR5235987' has 0 unresolved dependencies Read 18120705 spots for SRR5235987/SRR5235987.sra Written 18120705 spots for SRR5235987/SRR5235987.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: 00:06:18 18120705 reads; of these: 18120705 (100.00%) were unpaired; of these: 1962650 (10.83%) aligned 0 times 13914919 (76.79%) aligned exactly 1 time 2243136 (12.38%) aligned >1 times 89.17% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 4848397 / 16158055 = 0.3001 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 08:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.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 08:19:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:10: 1000000 INFO @ Tue, 16 Jun 2020 08:19:16: 2000000 INFO @ Tue, 16 Jun 2020 08:19:22: 3000000 INFO @ Tue, 16 Jun 2020 08:19:28: 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 08:19:34: 5000000 INFO @ Tue, 16 Jun 2020 08:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.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 08:19:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:40: 6000000 INFO @ Tue, 16 Jun 2020 08:19:41: 1000000 INFO @ Tue, 16 Jun 2020 08:19:47: 7000000 INFO @ Tue, 16 Jun 2020 08:19:48: 2000000 INFO @ Tue, 16 Jun 2020 08:19:54: 8000000 INFO @ Tue, 16 Jun 2020 08:19:54: 3000000 INFO @ Tue, 16 Jun 2020 08:20:00: 9000000 INFO @ Tue, 16 Jun 2020 08:20:01: 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 08:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.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 08:20:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:07: 10000000 INFO @ Tue, 16 Jun 2020 08:20:07: 5000000 INFO @ Tue, 16 Jun 2020 08:20:11: 1000000 INFO @ Tue, 16 Jun 2020 08:20:13: 11000000 INFO @ Tue, 16 Jun 2020 08:20:14: 6000000 INFO @ Tue, 16 Jun 2020 08:20:15: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:20:15: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:20:15: #1 total tags in treatment: 11309658 INFO @ Tue, 16 Jun 2020 08:20:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:15: #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 08:20:15: #1 tags after filtering in treatment: 11309658 INFO @ Tue, 16 Jun 2020 08:20:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:16: #2 number of paired peaks: 412 WARNING @ Tue, 16 Jun 2020 08:20:16: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:16: #2 predicted fragment length is 100 bps INFO @ Tue, 16 Jun 2020 08:20:16: #2 alternative fragment length(s) may be 3,100 bps INFO @ Tue, 16 Jun 2020 08:20:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:16: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:16: #2 You may need to consider one of the other alternative d(s): 3,100 WARNING @ Tue, 16 Jun 2020 08:20:16: #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 08:20:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:18: 2000000 INFO @ Tue, 16 Jun 2020 08:20:20: 7000000 INFO @ Tue, 16 Jun 2020 08:20:25: 3000000 INFO @ Tue, 16 Jun 2020 08:20:27: 8000000 INFO @ Tue, 16 Jun 2020 08:20:31: 4000000 INFO @ Tue, 16 Jun 2020 08:20:33: 9000000 INFO @ Tue, 16 Jun 2020 08:20:37: 5000000 INFO @ Tue, 16 Jun 2020 08:20:40: 10000000 INFO @ Tue, 16 Jun 2020 08:20:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:44: 6000000 INFO @ Tue, 16 Jun 2020 08:20:46: 11000000 INFO @ Tue, 16 Jun 2020 08:20:48: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:20:48: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:20:48: #1 total tags in treatment: 11309658 INFO @ Tue, 16 Jun 2020 08:20:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:48: #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 08:20:48: #1 tags after filtering in treatment: 11309658 INFO @ Tue, 16 Jun 2020 08:20:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:49: #2 number of paired peaks: 412 WARNING @ Tue, 16 Jun 2020 08:20:49: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:49: #2 predicted fragment length is 100 bps INFO @ Tue, 16 Jun 2020 08:20:49: #2 alternative fragment length(s) may be 3,100 bps INFO @ Tue, 16 Jun 2020 08:20:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:49: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:49: #2 You may need to consider one of the other alternative d(s): 3,100 WARNING @ Tue, 16 Jun 2020 08:20:49: #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 08:20:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:50: 7000000 INFO @ Tue, 16 Jun 2020 08:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4386 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:56: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:02: 9000000 INFO @ Tue, 16 Jun 2020 08:21:08: 10000000 INFO @ Tue, 16 Jun 2020 08:21:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:13: 11000000 INFO @ Tue, 16 Jun 2020 08:21:15: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:21:15: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:21:15: #1 total tags in treatment: 11309658 INFO @ Tue, 16 Jun 2020 08:21:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:15: #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 08:21:15: #1 tags after filtering in treatment: 11309658 INFO @ Tue, 16 Jun 2020 08:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:16: #2 number of paired peaks: 412 WARNING @ Tue, 16 Jun 2020 08:21:16: Fewer paired peaks (412) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 412 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:16: #2 predicted fragment length is 100 bps INFO @ Tue, 16 Jun 2020 08:21:16: #2 alternative fragment length(s) may be 3,100 bps INFO @ Tue, 16 Jun 2020 08:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:16: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:16: #2 You may need to consider one of the other alternative d(s): 3,100 WARNING @ Tue, 16 Jun 2020 08:21:16: #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 08:21:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1048 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543051/SRX2543051.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (173 records, 4 fields): 1 millis CompletedMACS2peakCalling