Job ID = 6497485 SRX = SRX495006 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:34:36 prefetch.2.10.7: 1) Downloading 'SRR1198538'... 2020-06-25T21:34:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:37:42 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:37:42 prefetch.2.10.7: 1) 'SRR1198538' was downloaded successfully Read 18057801 spots for SRR1198538/SRR1198538.sra Written 18057801 spots for SRR1198538/SRR1198538.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: 00:05:28 18057801 reads; of these: 18057801 (100.00%) were unpaired; of these: 112861 (0.62%) aligned 0 times 15059243 (83.39%) aligned exactly 1 time 2885697 (15.98%) aligned >1 times 99.38% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3187622 / 17944940 = 0.1776 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 06:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.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 06:50:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:50:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:50:21: 1000000 INFO @ Fri, 26 Jun 2020 06:50:27: 2000000 INFO @ Fri, 26 Jun 2020 06:50:32: 3000000 INFO @ Fri, 26 Jun 2020 06:50:37: 4000000 INFO @ Fri, 26 Jun 2020 06:50:42: 5000000 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 06:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.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 06:50:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:50:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:50:48: 6000000 INFO @ Fri, 26 Jun 2020 06:50:51: 1000000 INFO @ Fri, 26 Jun 2020 06:50:53: 7000000 INFO @ Fri, 26 Jun 2020 06:50:56: 2000000 INFO @ Fri, 26 Jun 2020 06:50:58: 8000000 INFO @ Fri, 26 Jun 2020 06:51:01: 3000000 INFO @ Fri, 26 Jun 2020 06:51:03: 9000000 INFO @ Fri, 26 Jun 2020 06:51:06: 4000000 INFO @ Fri, 26 Jun 2020 06:51:09: 10000000 INFO @ Fri, 26 Jun 2020 06:51:11: 5000000 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 06:51:14: 11000000 INFO @ Fri, 26 Jun 2020 06:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.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 06:51:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:51:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:51:16: 6000000 INFO @ Fri, 26 Jun 2020 06:51:20: 12000000 INFO @ Fri, 26 Jun 2020 06:51:21: 1000000 INFO @ Fri, 26 Jun 2020 06:51:22: 7000000 INFO @ Fri, 26 Jun 2020 06:51:25: 13000000 INFO @ Fri, 26 Jun 2020 06:51:26: 2000000 INFO @ Fri, 26 Jun 2020 06:51:27: 8000000 INFO @ Fri, 26 Jun 2020 06:51:30: 14000000 INFO @ Fri, 26 Jun 2020 06:51:31: 3000000 INFO @ Fri, 26 Jun 2020 06:51:32: 9000000 INFO @ Fri, 26 Jun 2020 06:51:34: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:51:34: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:51:34: #1 total tags in treatment: 14757318 INFO @ Fri, 26 Jun 2020 06:51:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:51:34: #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 06:51:35: #1 tags after filtering in treatment: 14757318 INFO @ Fri, 26 Jun 2020 06:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:51:35: #1 finished! INFO @ Fri, 26 Jun 2020 06:51:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:51:36: #2 number of paired peaks: 262 WARNING @ Fri, 26 Jun 2020 06:51:36: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Fri, 26 Jun 2020 06:51:36: start model_add_line... INFO @ Fri, 26 Jun 2020 06:51:36: start X-correlation... INFO @ Fri, 26 Jun 2020 06:51:36: end of X-cor INFO @ Fri, 26 Jun 2020 06:51:36: #2 finished! INFO @ Fri, 26 Jun 2020 06:51:36: #2 predicted fragment length is 39 bps INFO @ Fri, 26 Jun 2020 06:51:36: #2 alternative fragment length(s) may be 1,39,551 bps INFO @ Fri, 26 Jun 2020 06:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.05_model.r WARNING @ Fri, 26 Jun 2020 06:51:36: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:51:36: #2 You may need to consider one of the other alternative d(s): 1,39,551 WARNING @ Fri, 26 Jun 2020 06:51:36: #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 06:51:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:51:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:51:37: 4000000 INFO @ Fri, 26 Jun 2020 06:51:38: 10000000 INFO @ Fri, 26 Jun 2020 06:51:42: 5000000 INFO @ Fri, 26 Jun 2020 06:51:43: 11000000 INFO @ Fri, 26 Jun 2020 06:51:47: 6000000 INFO @ Fri, 26 Jun 2020 06:51:48: 12000000 INFO @ Fri, 26 Jun 2020 06:51:52: 7000000 INFO @ Fri, 26 Jun 2020 06:51:53: 13000000 INFO @ Fri, 26 Jun 2020 06:51:58: 8000000 INFO @ Fri, 26 Jun 2020 06:51:58: 14000000 INFO @ Fri, 26 Jun 2020 06:52:02: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:52:02: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:52:02: #1 total tags in treatment: 14757318 INFO @ Fri, 26 Jun 2020 06:52:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:52:02: #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 06:52:02: #1 tags after filtering in treatment: 14757318 INFO @ Fri, 26 Jun 2020 06:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:52:02: #1 finished! INFO @ Fri, 26 Jun 2020 06:52:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:52:03: 9000000 INFO @ Fri, 26 Jun 2020 06:52:03: #2 number of paired peaks: 262 WARNING @ Fri, 26 Jun 2020 06:52:03: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Fri, 26 Jun 2020 06:52:03: start model_add_line... INFO @ Fri, 26 Jun 2020 06:52:04: start X-correlation... INFO @ Fri, 26 Jun 2020 06:52:04: end of X-cor INFO @ Fri, 26 Jun 2020 06:52:04: #2 finished! INFO @ Fri, 26 Jun 2020 06:52:04: #2 predicted fragment length is 39 bps INFO @ Fri, 26 Jun 2020 06:52:04: #2 alternative fragment length(s) may be 1,39,551 bps INFO @ Fri, 26 Jun 2020 06:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.10_model.r INFO @ Fri, 26 Jun 2020 06:52:04: #3 Call peaks for each chromosome... WARNING @ Fri, 26 Jun 2020 06:52:05: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:52:05: #2 You may need to consider one of the other alternative d(s): 1,39,551 WARNING @ Fri, 26 Jun 2020 06:52:05: #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 06:52:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:52:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:52:08: 10000000 INFO @ Fri, 26 Jun 2020 06:52:14: 11000000 INFO @ Fri, 26 Jun 2020 06:52:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:52:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:52:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.05_summits.bed INFO @ Fri, 26 Jun 2020 06:52:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 5 millis INFO @ Fri, 26 Jun 2020 06:52:19: 12000000 CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:52:24: 13000000 INFO @ Fri, 26 Jun 2020 06:52:29: 14000000 INFO @ Fri, 26 Jun 2020 06:52:33: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 06:52:33: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 06:52:33: #1 total tags in treatment: 14757318 INFO @ Fri, 26 Jun 2020 06:52:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:52:33: #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 06:52:33: #1 tags after filtering in treatment: 14757318 INFO @ Fri, 26 Jun 2020 06:52:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:52:33: #1 finished! INFO @ Fri, 26 Jun 2020 06:52:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:52:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:52:34: #2 number of paired peaks: 262 WARNING @ Fri, 26 Jun 2020 06:52:34: Fewer paired peaks (262) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 262 pairs to build model! INFO @ Fri, 26 Jun 2020 06:52:34: start model_add_line... INFO @ Fri, 26 Jun 2020 06:52:34: start X-correlation... INFO @ Fri, 26 Jun 2020 06:52:34: end of X-cor INFO @ Fri, 26 Jun 2020 06:52:34: #2 finished! INFO @ Fri, 26 Jun 2020 06:52:34: #2 predicted fragment length is 39 bps INFO @ Fri, 26 Jun 2020 06:52:34: #2 alternative fragment length(s) may be 1,39,551 bps INFO @ Fri, 26 Jun 2020 06:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.20_model.r BedGraph に変換しました。 BigWig に変換中... WARNING @ Fri, 26 Jun 2020 06:52:39: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:52:39: #2 You may need to consider one of the other alternative d(s): 1,39,551 WARNING @ Fri, 26 Jun 2020 06:52:39: #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 06:52:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:52:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.10_summits.bed INFO @ Fri, 26 Jun 2020 06:52:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:53:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495006/SRX495006.20_summits.bed INFO @ Fri, 26 Jun 2020 06:53:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (103 records, 4 fields): 1 millis CompletedMACS2peakCalling