Job ID = 6507908 SRX = SRX495010 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:25:48 prefetch.2.10.7: 1) Downloading 'SRR1198542'... 2020-06-26T13:25:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:27:19 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:27:20 prefetch.2.10.7: 'SRR1198542' is valid 2020-06-26T13:27:20 prefetch.2.10.7: 1) 'SRR1198542' was downloaded successfully Read 13338445 spots for SRR1198542/SRR1198542.sra Written 13338445 spots for SRR1198542/SRR1198542.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: 00:00:01 Multiseed full-index search: 00:02:44 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 88325 (0.66%) aligned 0 times 10992861 (82.41%) aligned exactly 1 time 2257259 (16.92%) aligned >1 times 99.34% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 2113821 / 13250120 = 0.1595 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 22:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.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 22:34:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:34:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:19: 1000000 INFO @ Fri, 26 Jun 2020 22:34:26: 2000000 INFO @ Fri, 26 Jun 2020 22:34:32: 3000000 INFO @ Fri, 26 Jun 2020 22:34:38: 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 22:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.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 22:34:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:34:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:34:45: 5000000 INFO @ Fri, 26 Jun 2020 22:34:49: 1000000 INFO @ Fri, 26 Jun 2020 22:34:52: 6000000 INFO @ Fri, 26 Jun 2020 22:34:56: 2000000 INFO @ Fri, 26 Jun 2020 22:34:59: 7000000 INFO @ Fri, 26 Jun 2020 22:35:03: 3000000 INFO @ Fri, 26 Jun 2020 22:35:06: 8000000 INFO @ Fri, 26 Jun 2020 22:35:10: 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 @ Fri, 26 Jun 2020 22:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.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 22:35:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:35:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:35:13: 9000000 INFO @ Fri, 26 Jun 2020 22:35:17: 5000000 INFO @ Fri, 26 Jun 2020 22:35:21: 1000000 INFO @ Fri, 26 Jun 2020 22:35:21: 10000000 INFO @ Fri, 26 Jun 2020 22:35:24: 6000000 INFO @ Fri, 26 Jun 2020 22:35:28: 11000000 INFO @ Fri, 26 Jun 2020 22:35:28: 2000000 INFO @ Fri, 26 Jun 2020 22:35:29: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:35:29: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:35:29: #1 total tags in treatment: 11136299 INFO @ Fri, 26 Jun 2020 22:35:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:35:29: #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 22:35:29: #1 tags after filtering in treatment: 11136299 INFO @ Fri, 26 Jun 2020 22:35:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:35:29: #1 finished! INFO @ Fri, 26 Jun 2020 22:35:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:35:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:35:30: #2 number of paired peaks: 367 WARNING @ Fri, 26 Jun 2020 22:35:30: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Fri, 26 Jun 2020 22:35:30: start model_add_line... INFO @ Fri, 26 Jun 2020 22:35:30: start X-correlation... INFO @ Fri, 26 Jun 2020 22:35:30: end of X-cor INFO @ Fri, 26 Jun 2020 22:35:30: #2 finished! INFO @ Fri, 26 Jun 2020 22:35:30: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:35:30: #2 alternative fragment length(s) may be 2,44,557,567,570 bps INFO @ Fri, 26 Jun 2020 22:35:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.05_model.r WARNING @ Fri, 26 Jun 2020 22:35:30: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:35:30: #2 You may need to consider one of the other alternative d(s): 2,44,557,567,570 WARNING @ Fri, 26 Jun 2020 22:35:30: #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 22:35:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:35:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:35:31: 7000000 INFO @ Fri, 26 Jun 2020 22:35:36: 3000000 INFO @ Fri, 26 Jun 2020 22:35:38: 8000000 INFO @ Fri, 26 Jun 2020 22:35:44: 4000000 INFO @ Fri, 26 Jun 2020 22:35:46: 9000000 INFO @ Fri, 26 Jun 2020 22:35:51: 5000000 INFO @ Fri, 26 Jun 2020 22:35:53: 10000000 INFO @ Fri, 26 Jun 2020 22:35:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:35:59: 6000000 INFO @ Fri, 26 Jun 2020 22:36:00: 11000000 INFO @ Fri, 26 Jun 2020 22:36:01: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:36:01: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:36:01: #1 total tags in treatment: 11136299 INFO @ Fri, 26 Jun 2020 22:36:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:01: #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 22:36:01: #1 tags after filtering in treatment: 11136299 INFO @ Fri, 26 Jun 2020 22:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:36:01: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:02: #2 number of paired peaks: 367 WARNING @ Fri, 26 Jun 2020 22:36:02: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Fri, 26 Jun 2020 22:36:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:02: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:36:02: #2 alternative fragment length(s) may be 2,44,557,567,570 bps INFO @ Fri, 26 Jun 2020 22:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.10_model.r WARNING @ Fri, 26 Jun 2020 22:36:02: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:36:02: #2 You may need to consider one of the other alternative d(s): 2,44,557,567,570 WARNING @ Fri, 26 Jun 2020 22:36:02: #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 22:36:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:36:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:36:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:36:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.05_summits.bed INFO @ Fri, 26 Jun 2020 22:36:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (968 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:36:06: 7000000 INFO @ Fri, 26 Jun 2020 22:36:13: 8000000 INFO @ Fri, 26 Jun 2020 22:36:20: 9000000 INFO @ Fri, 26 Jun 2020 22:36:27: 10000000 INFO @ Fri, 26 Jun 2020 22:36:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:36:34: 11000000 INFO @ Fri, 26 Jun 2020 22:36:35: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 22:36:35: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 22:36:35: #1 total tags in treatment: 11136299 INFO @ Fri, 26 Jun 2020 22:36:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:36:35: #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 22:36:35: #1 tags after filtering in treatment: 11136299 INFO @ Fri, 26 Jun 2020 22:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:36:35: #1 finished! INFO @ Fri, 26 Jun 2020 22:36:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:36:36: #2 number of paired peaks: 367 WARNING @ Fri, 26 Jun 2020 22:36:36: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Fri, 26 Jun 2020 22:36:36: start model_add_line... INFO @ Fri, 26 Jun 2020 22:36:36: start X-correlation... INFO @ Fri, 26 Jun 2020 22:36:36: end of X-cor INFO @ Fri, 26 Jun 2020 22:36:36: #2 finished! INFO @ Fri, 26 Jun 2020 22:36:36: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:36:36: #2 alternative fragment length(s) may be 2,44,557,567,570 bps INFO @ Fri, 26 Jun 2020 22:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.20_model.r WARNING @ Fri, 26 Jun 2020 22:36:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:36:36: #2 You may need to consider one of the other alternative d(s): 2,44,557,567,570 WARNING @ Fri, 26 Jun 2020 22:36:36: #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 22:36:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.10_summits.bed INFO @ Fri, 26 Jun 2020 22:36:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (378 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:36:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495010/SRX495010.20_summits.bed INFO @ Fri, 26 Jun 2020 22:37:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (155 records, 4 fields): 2 millis CompletedMACS2peakCalling