Job ID = 6367995 SRX = SRX466458 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:52:48 prefetch.2.10.7: 1) Downloading 'SRR1163524'... 2020-06-15T23:52:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:29 prefetch.2.10.7: 1) 'SRR1163524' was downloaded successfully Read 34284849 spots for SRR1163524/SRR1163524.sra Written 34284849 spots for SRR1163524/SRR1163524.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: 00:06:49 34284849 reads; of these: 34284849 (100.00%) were unpaired; of these: 6795002 (19.82%) aligned 0 times 23736405 (69.23%) aligned exactly 1 time 3753442 (10.95%) aligned >1 times 80.18% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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_sort_core] merging from 12 files... [bam_rmdupse_core] 10218995 / 27489847 = 0.3717 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 09:10:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.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 09:10:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:05: 1000000 INFO @ Tue, 16 Jun 2020 09:10:11: 2000000 INFO @ Tue, 16 Jun 2020 09:10:16: 3000000 INFO @ Tue, 16 Jun 2020 09:10:21: 4000000 INFO @ Tue, 16 Jun 2020 09:10:26: 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 @ Tue, 16 Jun 2020 09:10:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.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 09:10:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:32: 6000000 INFO @ Tue, 16 Jun 2020 09:10:36: 1000000 INFO @ Tue, 16 Jun 2020 09:10:37: 7000000 INFO @ Tue, 16 Jun 2020 09:10:41: 2000000 INFO @ Tue, 16 Jun 2020 09:10:43: 8000000 INFO @ Tue, 16 Jun 2020 09:10:47: 3000000 INFO @ Tue, 16 Jun 2020 09:10:49: 9000000 INFO @ Tue, 16 Jun 2020 09:10:52: 4000000 INFO @ Tue, 16 Jun 2020 09:10:54: 10000000 INFO @ Tue, 16 Jun 2020 09:10:58: 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 @ Tue, 16 Jun 2020 09:11:00: 11000000 INFO @ Tue, 16 Jun 2020 09:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.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 09:11:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:04: 6000000 INFO @ Tue, 16 Jun 2020 09:11:06: 12000000 INFO @ Tue, 16 Jun 2020 09:11:06: 1000000 INFO @ Tue, 16 Jun 2020 09:11:10: 7000000 INFO @ Tue, 16 Jun 2020 09:11:12: 13000000 INFO @ Tue, 16 Jun 2020 09:11:12: 2000000 INFO @ Tue, 16 Jun 2020 09:11:16: 8000000 INFO @ Tue, 16 Jun 2020 09:11:18: 14000000 INFO @ Tue, 16 Jun 2020 09:11:18: 3000000 INFO @ Tue, 16 Jun 2020 09:11:21: 9000000 INFO @ Tue, 16 Jun 2020 09:11:24: 15000000 INFO @ Tue, 16 Jun 2020 09:11:24: 4000000 INFO @ Tue, 16 Jun 2020 09:11:27: 10000000 INFO @ Tue, 16 Jun 2020 09:11:29: 16000000 INFO @ Tue, 16 Jun 2020 09:11:30: 5000000 INFO @ Tue, 16 Jun 2020 09:11:33: 11000000 INFO @ Tue, 16 Jun 2020 09:11:35: 17000000 INFO @ Tue, 16 Jun 2020 09:11:35: 6000000 INFO @ Tue, 16 Jun 2020 09:11:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:37: #1 total tags in treatment: 17270852 INFO @ Tue, 16 Jun 2020 09:11:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:37: #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 09:11:37: #1 tags after filtering in treatment: 17270852 INFO @ Tue, 16 Jun 2020 09:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:38: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 09:11:38: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:38: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:11:38: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 09:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:38: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:38: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 09:11:38: #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 09:11:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:39: 12000000 INFO @ Tue, 16 Jun 2020 09:11:41: 7000000 INFO @ Tue, 16 Jun 2020 09:11:45: 13000000 INFO @ Tue, 16 Jun 2020 09:11:47: 8000000 INFO @ Tue, 16 Jun 2020 09:11:50: 14000000 INFO @ Tue, 16 Jun 2020 09:11:52: 9000000 INFO @ Tue, 16 Jun 2020 09:11:56: 15000000 INFO @ Tue, 16 Jun 2020 09:11:58: 10000000 INFO @ Tue, 16 Jun 2020 09:12:02: 16000000 INFO @ Tue, 16 Jun 2020 09:12:04: 11000000 INFO @ Tue, 16 Jun 2020 09:12:07: 17000000 INFO @ Tue, 16 Jun 2020 09:12:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:09: #1 total tags in treatment: 17270852 INFO @ Tue, 16 Jun 2020 09:12:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:09: #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 09:12:09: #1 tags after filtering in treatment: 17270852 INFO @ Tue, 16 Jun 2020 09:12:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:09: 12000000 INFO @ Tue, 16 Jun 2020 09:12:10: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 09:12:10: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:11: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:12:11: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 09:12:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:11: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:11: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 09:12:11: #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 09:12:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:15: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:21: 14000000 INFO @ Tue, 16 Jun 2020 09:12:26: 15000000 INFO @ Tue, 16 Jun 2020 09:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1400 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:32: 16000000 INFO @ Tue, 16 Jun 2020 09:12:37: 17000000 INFO @ Tue, 16 Jun 2020 09:12:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:39: #1 total tags in treatment: 17270852 INFO @ Tue, 16 Jun 2020 09:12:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:39: #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 09:12:39: #1 tags after filtering in treatment: 17270852 INFO @ Tue, 16 Jun 2020 09:12:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:40: #2 number of paired peaks: 186 WARNING @ Tue, 16 Jun 2020 09:12:40: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:40: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:12:40: #2 alternative fragment length(s) may be 2,46 bps INFO @ Tue, 16 Jun 2020 09:12:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:40: #2 You may need to consider one of the other alternative d(s): 2,46 WARNING @ Tue, 16 Jun 2020 09:12:40: #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 09:12:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (478 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466458/SRX466458.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 1 millis CompletedMACS2peakCalling