Job ID = 6497483 SRX = SRX495002 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:24:49 prefetch.2.10.7: 1) Downloading 'SRR1198534'... 2020-06-25T21:24:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:26:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:26:39 prefetch.2.10.7: 'SRR1198534' is valid 2020-06-25T21:26:39 prefetch.2.10.7: 1) 'SRR1198534' was downloaded successfully Read 13338445 spots for SRR1198534/SRR1198534.sra Written 13338445 spots for SRR1198534/SRR1198534.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: 00:02:54 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 89000 (0.67%) aligned 0 times 10992385 (82.41%) aligned exactly 1 time 2257060 (16.92%) aligned >1 times 99.33% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 2114313 / 13249445 = 0.1596 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 06:33:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.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 06:33:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:33:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:33:56: 1000000 INFO @ Fri, 26 Jun 2020 06:34:01: 2000000 INFO @ Fri, 26 Jun 2020 06:34:07: 3000000 INFO @ Fri, 26 Jun 2020 06:34:12: 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 06:34:18: 5000000 INFO @ Fri, 26 Jun 2020 06:34:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.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 06:34:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:34:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:34:24: 6000000 INFO @ Fri, 26 Jun 2020 06:34:25: 1000000 INFO @ Fri, 26 Jun 2020 06:34:30: 7000000 INFO @ Fri, 26 Jun 2020 06:34:32: 2000000 INFO @ Fri, 26 Jun 2020 06:34:36: 8000000 INFO @ Fri, 26 Jun 2020 06:34:38: 3000000 INFO @ Fri, 26 Jun 2020 06:34:42: 9000000 INFO @ Fri, 26 Jun 2020 06:34:44: 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 06:34:48: 10000000 INFO @ Fri, 26 Jun 2020 06:34:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.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 06:34:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:34:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:34:51: 5000000 INFO @ Fri, 26 Jun 2020 06:34:54: 11000000 INFO @ Fri, 26 Jun 2020 06:34:55: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:34:55: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:34:55: #1 total tags in treatment: 11135132 INFO @ Fri, 26 Jun 2020 06:34:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:34:55: #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 06:34:55: #1 tags after filtering in treatment: 11135132 INFO @ Fri, 26 Jun 2020 06:34:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:34:55: #1 finished! INFO @ Fri, 26 Jun 2020 06:34:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:34:56: 1000000 INFO @ Fri, 26 Jun 2020 06:34:56: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 06:34:56: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 06:34:56: start model_add_line... INFO @ Fri, 26 Jun 2020 06:34:56: start X-correlation... INFO @ Fri, 26 Jun 2020 06:34:56: end of X-cor INFO @ Fri, 26 Jun 2020 06:34:56: #2 finished! INFO @ Fri, 26 Jun 2020 06:34:56: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:34:56: #2 alternative fragment length(s) may be 2,40,592 bps INFO @ Fri, 26 Jun 2020 06:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.05_model.r WARNING @ Fri, 26 Jun 2020 06:34:56: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:34:56: #2 You may need to consider one of the other alternative d(s): 2,40,592 WARNING @ Fri, 26 Jun 2020 06:34:56: #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 06:34:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:34:57: 6000000 INFO @ Fri, 26 Jun 2020 06:35:02: 2000000 INFO @ Fri, 26 Jun 2020 06:35:03: 7000000 INFO @ Fri, 26 Jun 2020 06:35:08: 3000000 INFO @ Fri, 26 Jun 2020 06:35:10: 8000000 INFO @ Fri, 26 Jun 2020 06:35:14: 4000000 INFO @ Fri, 26 Jun 2020 06:35:17: 9000000 INFO @ Fri, 26 Jun 2020 06:35:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:35:20: 5000000 INFO @ Fri, 26 Jun 2020 06:35:23: 10000000 INFO @ Fri, 26 Jun 2020 06:35:26: 6000000 INFO @ Fri, 26 Jun 2020 06:35:30: 11000000 INFO @ Fri, 26 Jun 2020 06:35:30: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:35:30: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:35:30: #1 total tags in treatment: 11135132 INFO @ Fri, 26 Jun 2020 06:35:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:35:30: #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 06:35:31: #1 tags after filtering in treatment: 11135132 INFO @ Fri, 26 Jun 2020 06:35:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:35:31: #1 finished! INFO @ Fri, 26 Jun 2020 06:35:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:35:31: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 06:35:31: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 06:35:31: start model_add_line... INFO @ Fri, 26 Jun 2020 06:35:32: start X-correlation... INFO @ Fri, 26 Jun 2020 06:35:32: end of X-cor INFO @ Fri, 26 Jun 2020 06:35:32: #2 finished! INFO @ Fri, 26 Jun 2020 06:35:32: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:35:32: #2 alternative fragment length(s) may be 2,40,592 bps INFO @ Fri, 26 Jun 2020 06:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.10_model.r WARNING @ Fri, 26 Jun 2020 06:35:32: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:35:32: #2 You may need to consider one of the other alternative d(s): 2,40,592 WARNING @ Fri, 26 Jun 2020 06:35:32: #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 06:35:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:35:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:35:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:35:32: 7000000 INFO @ Fri, 26 Jun 2020 06:35:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:35:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.05_summits.bed INFO @ Fri, 26 Jun 2020 06:35:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:35:38: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:35:43: 9000000 INFO @ Fri, 26 Jun 2020 06:35:49: 10000000 INFO @ Fri, 26 Jun 2020 06:35:55: 11000000 INFO @ Fri, 26 Jun 2020 06:35:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:35:55: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:35:55: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:35:55: #1 total tags in treatment: 11135132 INFO @ Fri, 26 Jun 2020 06:35:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:35:55: #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 06:35:55: #1 tags after filtering in treatment: 11135132 INFO @ Fri, 26 Jun 2020 06:35:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:35:55: #1 finished! INFO @ Fri, 26 Jun 2020 06:35:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:35:56: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 06:35:56: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 06:35:56: start model_add_line... INFO @ Fri, 26 Jun 2020 06:35:56: start X-correlation... INFO @ Fri, 26 Jun 2020 06:35:56: end of X-cor INFO @ Fri, 26 Jun 2020 06:35:56: #2 finished! INFO @ Fri, 26 Jun 2020 06:35:56: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:35:56: #2 alternative fragment length(s) may be 2,40,592 bps INFO @ Fri, 26 Jun 2020 06:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.20_model.r INFO @ Fri, 26 Jun 2020 06:36:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.10_peaks.narrowPeak WARNING @ Fri, 26 Jun 2020 06:36:20: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:36:20: #2 You may need to consider one of the other alternative d(s): 2,40,592 WARNING @ Fri, 26 Jun 2020 06:36:20: #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 06:36:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:36:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:36:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.10_summits.bed INFO @ Fri, 26 Jun 2020 06:36:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (361 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:36:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:36:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:37:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:37:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495002/SRX495002.20_summits.bed INFO @ Fri, 26 Jun 2020 06:37:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (129 records, 4 fields): 53928 millis CompletedMACS2peakCalling