Job ID = 6367764 SRX = SRX4082378 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:35 prefetch.2.10.7: 1) Downloading 'SRR7164196'... 2020-06-15T23:32:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:38 prefetch.2.10.7: 'SRR7164196' is valid 2020-06-15T23:34:38 prefetch.2.10.7: 1) 'SRR7164196' was downloaded successfully 2020-06-15T23:34:38 prefetch.2.10.7: 'SRR7164196' has 0 unresolved dependencies Read 17374970 spots for SRR7164196/SRR7164196.sra Written 17374970 spots for SRR7164196/SRR7164196.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: 00:03:59 17374970 reads; of these: 17374970 (100.00%) were unpaired; of these: 521082 (3.00%) aligned 0 times 12895050 (74.22%) aligned exactly 1 time 3958838 (22.78%) aligned >1 times 97.00% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 2934186 / 16853888 = 0.1741 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 08:43:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.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 08:43:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:45: 1000000 INFO @ Tue, 16 Jun 2020 08:43:50: 2000000 INFO @ Tue, 16 Jun 2020 08:43:55: 3000000 INFO @ Tue, 16 Jun 2020 08:44:00: 4000000 INFO @ Tue, 16 Jun 2020 08:44:05: 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 08:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.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 08:44:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:10: 6000000 INFO @ Tue, 16 Jun 2020 08:44:16: 1000000 INFO @ Tue, 16 Jun 2020 08:44:16: 7000000 INFO @ Tue, 16 Jun 2020 08:44:22: 2000000 INFO @ Tue, 16 Jun 2020 08:44:22: 8000000 INFO @ Tue, 16 Jun 2020 08:44:27: 3000000 INFO @ Tue, 16 Jun 2020 08:44:28: 9000000 INFO @ Tue, 16 Jun 2020 08:44:33: 4000000 INFO @ Tue, 16 Jun 2020 08:44:33: 10000000 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 08:44:39: 5000000 INFO @ Tue, 16 Jun 2020 08:44:39: 11000000 INFO @ Tue, 16 Jun 2020 08:44:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.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 08:44:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:45: 6000000 INFO @ Tue, 16 Jun 2020 08:44:45: 12000000 INFO @ Tue, 16 Jun 2020 08:44:46: 1000000 INFO @ Tue, 16 Jun 2020 08:44:51: 7000000 INFO @ Tue, 16 Jun 2020 08:44:51: 13000000 INFO @ Tue, 16 Jun 2020 08:44:52: 2000000 INFO @ Tue, 16 Jun 2020 08:44:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:44:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:44:56: #1 total tags in treatment: 13919702 INFO @ Tue, 16 Jun 2020 08:44:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:56: #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 08:44:56: #1 tags after filtering in treatment: 13919702 INFO @ Tue, 16 Jun 2020 08:44:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:56: 8000000 INFO @ Tue, 16 Jun 2020 08:44:57: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:44:57: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:57: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 08:44:57: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 16 Jun 2020 08:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.05_model.r WARNING @ Tue, 16 Jun 2020 08:44:57: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:57: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 16 Jun 2020 08:44:57: #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 08:44:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:58: 3000000 INFO @ Tue, 16 Jun 2020 08:45:02: 9000000 INFO @ Tue, 16 Jun 2020 08:45:03: 4000000 INFO @ Tue, 16 Jun 2020 08:45:08: 10000000 INFO @ Tue, 16 Jun 2020 08:45:09: 5000000 INFO @ Tue, 16 Jun 2020 08:45:14: 11000000 INFO @ Tue, 16 Jun 2020 08:45:15: 6000000 INFO @ Tue, 16 Jun 2020 08:45:20: 12000000 INFO @ Tue, 16 Jun 2020 08:45:21: 7000000 INFO @ Tue, 16 Jun 2020 08:45:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:26: 13000000 INFO @ Tue, 16 Jun 2020 08:45:26: 8000000 INFO @ Tue, 16 Jun 2020 08:45:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:31: #1 total tags in treatment: 13919702 INFO @ Tue, 16 Jun 2020 08:45:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:31: #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 08:45:32: #1 tags after filtering in treatment: 13919702 INFO @ Tue, 16 Jun 2020 08:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:32: 9000000 INFO @ Tue, 16 Jun 2020 08:45:33: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:45:33: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:33: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 08:45:33: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 16 Jun 2020 08:45:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.10_model.r WARNING @ Tue, 16 Jun 2020 08:45:33: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:33: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 16 Jun 2020 08:45:33: #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 08:45:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:36: Done! INFO @ Tue, 16 Jun 2020 08:45:38: 10000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (891 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:45:43: 11000000 INFO @ Tue, 16 Jun 2020 08:45:49: 12000000 INFO @ Tue, 16 Jun 2020 08:45:54: 13000000 INFO @ Tue, 16 Jun 2020 08:45:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:45:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:45:59: #1 total tags in treatment: 13919702 INFO @ Tue, 16 Jun 2020 08:45:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:59: #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 08:45:59: #1 tags after filtering in treatment: 13919702 INFO @ Tue, 16 Jun 2020 08:45:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:00: #2 number of paired peaks: 396 WARNING @ Tue, 16 Jun 2020 08:46:00: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:00: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 08:46:00: #2 alternative fragment length(s) may be 2,39 bps INFO @ Tue, 16 Jun 2020 08:46:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.20_model.r WARNING @ Tue, 16 Jun 2020 08:46:00: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:00: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Tue, 16 Jun 2020 08:46:00: #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 08:46:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:46:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082378/SRX4082378.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling