Job ID = 6367219 SRX = SRX3043405 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:46 prefetch.2.10.7: 1) Downloading 'SRR5875889'... 2020-06-15T23:15:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:16 prefetch.2.10.7: 1) 'SRR5875889' was downloaded successfully Read 20483491 spots for SRR5875889/SRR5875889.sra Written 20483491 spots for SRR5875889/SRR5875889.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: 00:05:48 20483491 reads; of these: 20483491 (100.00%) were unpaired; of these: 348058 (1.70%) aligned 0 times 16963972 (82.82%) aligned exactly 1 time 3171461 (15.48%) aligned >1 times 98.30% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 4187588 / 20135433 = 0.2080 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 08:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.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 08:30:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:38: 1000000 INFO @ Tue, 16 Jun 2020 08:30:44: 2000000 INFO @ Tue, 16 Jun 2020 08:30:50: 3000000 INFO @ Tue, 16 Jun 2020 08:30:55: 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 08:31:01: 5000000 INFO @ Tue, 16 Jun 2020 08:31:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.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 08:31:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:08: 6000000 INFO @ Tue, 16 Jun 2020 08:31:09: 1000000 INFO @ Tue, 16 Jun 2020 08:31:15: 7000000 INFO @ Tue, 16 Jun 2020 08:31:15: 2000000 INFO @ Tue, 16 Jun 2020 08:31:21: 8000000 INFO @ Tue, 16 Jun 2020 08:31:22: 3000000 INFO @ Tue, 16 Jun 2020 08:31:28: 9000000 INFO @ Tue, 16 Jun 2020 08:31:29: 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 08:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.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 08:31:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:35: 10000000 INFO @ Tue, 16 Jun 2020 08:31:36: 5000000 INFO @ Tue, 16 Jun 2020 08:31:40: 1000000 INFO @ Tue, 16 Jun 2020 08:31:42: 11000000 INFO @ Tue, 16 Jun 2020 08:31:43: 6000000 INFO @ Tue, 16 Jun 2020 08:31:48: 2000000 INFO @ Tue, 16 Jun 2020 08:31:48: 12000000 INFO @ Tue, 16 Jun 2020 08:31:50: 7000000 INFO @ Tue, 16 Jun 2020 08:31:56: 13000000 INFO @ Tue, 16 Jun 2020 08:31:56: 3000000 INFO @ Tue, 16 Jun 2020 08:31:57: 8000000 INFO @ Tue, 16 Jun 2020 08:32:03: 14000000 INFO @ Tue, 16 Jun 2020 08:32:04: 4000000 INFO @ Tue, 16 Jun 2020 08:32:04: 9000000 INFO @ Tue, 16 Jun 2020 08:32:10: 15000000 INFO @ Tue, 16 Jun 2020 08:32:11: 10000000 INFO @ Tue, 16 Jun 2020 08:32:11: 5000000 INFO @ Tue, 16 Jun 2020 08:32:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:17: #1 total tags in treatment: 15947845 INFO @ Tue, 16 Jun 2020 08:32:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:17: #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 08:32:17: #1 tags after filtering in treatment: 15947845 INFO @ Tue, 16 Jun 2020 08:32:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:18: #2 number of paired peaks: 125 WARNING @ Tue, 16 Jun 2020 08:32:18: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:18: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 08:32:18: #2 alternative fragment length(s) may be 2,32,54,289,481,505,533,579,581,588,592 bps INFO @ Tue, 16 Jun 2020 08:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:18: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:18: #2 You may need to consider one of the other alternative d(s): 2,32,54,289,481,505,533,579,581,588,592 WARNING @ Tue, 16 Jun 2020 08:32:18: #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 08:32:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:18: 11000000 INFO @ Tue, 16 Jun 2020 08:32:19: 6000000 INFO @ Tue, 16 Jun 2020 08:32:25: 12000000 INFO @ Tue, 16 Jun 2020 08:32:27: 7000000 INFO @ Tue, 16 Jun 2020 08:32:32: 13000000 INFO @ Tue, 16 Jun 2020 08:32:35: 8000000 INFO @ Tue, 16 Jun 2020 08:32:39: 14000000 INFO @ Tue, 16 Jun 2020 08:32:42: 9000000 INFO @ Tue, 16 Jun 2020 08:32:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:46: 15000000 INFO @ Tue, 16 Jun 2020 08:32:50: 10000000 INFO @ Tue, 16 Jun 2020 08:32:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:52: #1 total tags in treatment: 15947845 INFO @ Tue, 16 Jun 2020 08:32:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:52: #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 08:32:53: #1 tags after filtering in treatment: 15947845 INFO @ Tue, 16 Jun 2020 08:32:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:54: #2 number of paired peaks: 125 WARNING @ Tue, 16 Jun 2020 08:32:54: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:54: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 08:32:54: #2 alternative fragment length(s) may be 2,32,54,289,481,505,533,579,581,588,592 bps INFO @ Tue, 16 Jun 2020 08:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:54: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:54: #2 You may need to consider one of the other alternative d(s): 2,32,54,289,481,505,533,579,581,588,592 WARNING @ Tue, 16 Jun 2020 08:32:54: #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 08:32:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:57: 11000000 INFO @ Tue, 16 Jun 2020 08:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.05_summits.bed INFO @ Tue, 16 Jun 2020 08:32:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:04: 12000000 INFO @ Tue, 16 Jun 2020 08:33:11: 13000000 INFO @ Tue, 16 Jun 2020 08:33:18: 14000000 INFO @ Tue, 16 Jun 2020 08:33:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:26: 15000000 INFO @ Tue, 16 Jun 2020 08:33:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:33:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:33:32: #1 total tags in treatment: 15947845 INFO @ Tue, 16 Jun 2020 08:33:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:32: #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 08:33:33: #1 tags after filtering in treatment: 15947845 INFO @ Tue, 16 Jun 2020 08:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:34: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:34: #2 number of paired peaks: 125 WARNING @ Tue, 16 Jun 2020 08:33:34: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:34: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 08:33:34: #2 alternative fragment length(s) may be 2,32,54,289,481,505,533,579,581,588,592 bps INFO @ Tue, 16 Jun 2020 08:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:34: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:34: #2 You may need to consider one of the other alternative d(s): 2,32,54,289,481,505,533,579,581,588,592 WARNING @ Tue, 16 Jun 2020 08:33:34: #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 08:33:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043405/SRX3043405.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 1 millis CompletedMACS2peakCalling