Job ID = 6368300 SRX = SRX494983 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:33 prefetch.2.10.7: 1) Downloading 'SRR1198515'... 2020-06-16T00:24:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:47 prefetch.2.10.7: 'SRR1198515' is valid 2020-06-16T00:25:47 prefetch.2.10.7: 1) 'SRR1198515' was downloaded successfully Read 13681916 spots for SRR1198515/SRR1198515.sra Written 13681916 spots for SRR1198515/SRR1198515.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: 00:02:49 13681916 reads; of these: 13681916 (100.00%) were unpaired; of these: 324880 (2.37%) aligned 0 times 10846913 (79.28%) aligned exactly 1 time 2510123 (18.35%) aligned >1 times 97.63% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 2389623 / 13357036 = 0.1789 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 09:32:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.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 09:32:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:38: 1000000 INFO @ Tue, 16 Jun 2020 09:32:45: 2000000 INFO @ Tue, 16 Jun 2020 09:32:51: 3000000 INFO @ Tue, 16 Jun 2020 09:32:58: 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 09:33:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.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 09:33:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:04: 5000000 INFO @ Tue, 16 Jun 2020 09:33:08: 1000000 INFO @ Tue, 16 Jun 2020 09:33:11: 6000000 INFO @ Tue, 16 Jun 2020 09:33:15: 2000000 INFO @ Tue, 16 Jun 2020 09:33:18: 7000000 INFO @ Tue, 16 Jun 2020 09:33:22: 3000000 INFO @ Tue, 16 Jun 2020 09:33:25: 8000000 INFO @ Tue, 16 Jun 2020 09:33:29: 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 09:33:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.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 09:33:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:32: 9000000 INFO @ Tue, 16 Jun 2020 09:33:36: 5000000 INFO @ Tue, 16 Jun 2020 09:33:38: 1000000 INFO @ Tue, 16 Jun 2020 09:33:39: 10000000 INFO @ Tue, 16 Jun 2020 09:33:43: 6000000 INFO @ Tue, 16 Jun 2020 09:33:44: 2000000 INFO @ Tue, 16 Jun 2020 09:33:46: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:33:46: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:33:46: #1 total tags in treatment: 10967413 INFO @ Tue, 16 Jun 2020 09:33:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:46: #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 09:33:46: #1 tags after filtering in treatment: 10967413 INFO @ Tue, 16 Jun 2020 09:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:47: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 09:33:47: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:47: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:33:47: #2 alternative fragment length(s) may be 4,51,66,595 bps INFO @ Tue, 16 Jun 2020 09:33:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:47: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:47: #2 You may need to consider one of the other alternative d(s): 4,51,66,595 WARNING @ Tue, 16 Jun 2020 09:33:47: #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 09:33:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:50: 7000000 INFO @ Tue, 16 Jun 2020 09:33:50: 3000000 INFO @ Tue, 16 Jun 2020 09:33:57: 4000000 INFO @ Tue, 16 Jun 2020 09:33:57: 8000000 INFO @ Tue, 16 Jun 2020 09:34:03: 5000000 INFO @ Tue, 16 Jun 2020 09:34:04: 9000000 INFO @ Tue, 16 Jun 2020 09:34:09: 6000000 INFO @ Tue, 16 Jun 2020 09:34:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:11: 10000000 INFO @ Tue, 16 Jun 2020 09:34:16: 7000000 INFO @ Tue, 16 Jun 2020 09:34:18: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:34:18: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:34:18: #1 total tags in treatment: 10967413 INFO @ Tue, 16 Jun 2020 09:34:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:18: #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 09:34:18: #1 tags after filtering in treatment: 10967413 INFO @ Tue, 16 Jun 2020 09:34:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:19: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 09:34:19: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:19: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:34:19: #2 alternative fragment length(s) may be 4,51,66,595 bps INFO @ Tue, 16 Jun 2020 09:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:19: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:19: #2 You may need to consider one of the other alternative d(s): 4,51,66,595 WARNING @ Tue, 16 Jun 2020 09:34:19: #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 09:34:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:34:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:22: Done! INFO @ Tue, 16 Jun 2020 09:34:22: 8000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4544 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:27: 9000000 INFO @ Tue, 16 Jun 2020 09:34:33: 10000000 INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:34:39: #1 total tags in treatment: 10967413 INFO @ Tue, 16 Jun 2020 09:34:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:39: #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 09:34:40: #1 tags after filtering in treatment: 10967413 INFO @ Tue, 16 Jun 2020 09:34:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:40: #2 number of paired peaks: 382 WARNING @ Tue, 16 Jun 2020 09:34:40: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2 alternative fragment length(s) may be 4,51,66,595 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.20_model.r WARNING @ Tue, 16 Jun 2020 09:34:40: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:40: #2 You may need to consider one of the other alternative d(s): 4,51,66,595 WARNING @ Tue, 16 Jun 2020 09:34:40: #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 09:34:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1052 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494983/SRX494983.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (266 records, 4 fields): 1 millis CompletedMACS2peakCalling