Job ID = 6367939 SRX = SRX4344426 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:34 prefetch.2.10.7: 1) Downloading 'SRR7474953'... 2020-06-16T00:27:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:35 prefetch.2.10.7: 1) 'SRR7474953' was downloaded successfully 2020-06-16T00:29:35 prefetch.2.10.7: 'SRR7474953' has 0 unresolved dependencies Read 21752982 spots for SRR7474953/SRR7474953.sra Written 21752982 spots for SRR7474953/SRR7474953.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: 00:04:59 21752982 reads; of these: 21752982 (100.00%) were unpaired; of these: 1048968 (4.82%) aligned 0 times 17892727 (82.25%) aligned exactly 1 time 2811287 (12.92%) aligned >1 times 95.18% overall alignment rate Time searching: 00:04:59 Overall time: 00:04:59 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 12 files... [bam_rmdupse_core] 2355180 / 20704014 = 0.1138 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 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.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 09:43:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:14: 1000000 INFO @ Tue, 16 Jun 2020 09:43:24: 2000000 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 09:43:33: 3000000 INFO @ Tue, 16 Jun 2020 09:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.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 09:43:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:42: 4000000 INFO @ Tue, 16 Jun 2020 09:43:43: 1000000 INFO @ Tue, 16 Jun 2020 09:43:51: 5000000 INFO @ Tue, 16 Jun 2020 09:43:52: 2000000 INFO @ Tue, 16 Jun 2020 09:43:59: 6000000 INFO @ Tue, 16 Jun 2020 09:44:01: 3000000 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 09:44:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.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 09:44:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:08: 7000000 INFO @ Tue, 16 Jun 2020 09:44:10: 4000000 INFO @ Tue, 16 Jun 2020 09:44:15: 1000000 INFO @ Tue, 16 Jun 2020 09:44:17: 8000000 INFO @ Tue, 16 Jun 2020 09:44:19: 5000000 INFO @ Tue, 16 Jun 2020 09:44:24: 2000000 INFO @ Tue, 16 Jun 2020 09:44:27: 9000000 INFO @ Tue, 16 Jun 2020 09:44:28: 6000000 INFO @ Tue, 16 Jun 2020 09:44:33: 3000000 INFO @ Tue, 16 Jun 2020 09:44:35: 10000000 INFO @ Tue, 16 Jun 2020 09:44:37: 7000000 INFO @ Tue, 16 Jun 2020 09:44:44: 4000000 INFO @ Tue, 16 Jun 2020 09:44:44: 11000000 INFO @ Tue, 16 Jun 2020 09:44:46: 8000000 INFO @ Tue, 16 Jun 2020 09:44:53: 5000000 INFO @ Tue, 16 Jun 2020 09:44:53: 12000000 INFO @ Tue, 16 Jun 2020 09:44:55: 9000000 INFO @ Tue, 16 Jun 2020 09:45:01: 6000000 INFO @ Tue, 16 Jun 2020 09:45:02: 13000000 INFO @ Tue, 16 Jun 2020 09:45:04: 10000000 INFO @ Tue, 16 Jun 2020 09:45:10: 7000000 INFO @ Tue, 16 Jun 2020 09:45:11: 14000000 INFO @ Tue, 16 Jun 2020 09:45:13: 11000000 INFO @ Tue, 16 Jun 2020 09:45:18: 8000000 INFO @ Tue, 16 Jun 2020 09:45:20: 15000000 INFO @ Tue, 16 Jun 2020 09:45:22: 12000000 INFO @ Tue, 16 Jun 2020 09:45:25: 9000000 INFO @ Tue, 16 Jun 2020 09:45:29: 16000000 INFO @ Tue, 16 Jun 2020 09:45:30: 13000000 INFO @ Tue, 16 Jun 2020 09:45:33: 10000000 INFO @ Tue, 16 Jun 2020 09:45:38: 17000000 INFO @ Tue, 16 Jun 2020 09:45:39: 14000000 INFO @ Tue, 16 Jun 2020 09:45:41: 11000000 INFO @ Tue, 16 Jun 2020 09:45:46: 18000000 INFO @ Tue, 16 Jun 2020 09:45:48: 15000000 INFO @ Tue, 16 Jun 2020 09:45:48: 12000000 INFO @ Tue, 16 Jun 2020 09:45:49: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:45:49: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:45:49: #1 total tags in treatment: 18348834 INFO @ Tue, 16 Jun 2020 09:45:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:49: #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 09:45:50: #1 tags after filtering in treatment: 18348834 INFO @ Tue, 16 Jun 2020 09:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:51: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 09:45:51: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:51: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:45:51: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.05_model.r WARNING @ Tue, 16 Jun 2020 09:45:51: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:51: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:45:51: #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 09:45:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:56: 13000000 INFO @ Tue, 16 Jun 2020 09:45:57: 16000000 INFO @ Tue, 16 Jun 2020 09:46:04: 14000000 INFO @ Tue, 16 Jun 2020 09:46:06: 17000000 INFO @ Tue, 16 Jun 2020 09:46:12: 15000000 INFO @ Tue, 16 Jun 2020 09:46:15: 18000000 INFO @ Tue, 16 Jun 2020 09:46:18: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:46:18: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:46:18: #1 total tags in treatment: 18348834 INFO @ Tue, 16 Jun 2020 09:46:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:18: #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 09:46:18: #1 tags after filtering in treatment: 18348834 INFO @ Tue, 16 Jun 2020 09:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:19: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 09:46:19: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:19: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:46:19: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:46:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.10_model.r WARNING @ Tue, 16 Jun 2020 09:46:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:19: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:46:19: #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 09:46:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:46:20: 16000000 INFO @ Tue, 16 Jun 2020 09:46:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:28: 17000000 INFO @ Tue, 16 Jun 2020 09:46:36: 18000000 INFO @ Tue, 16 Jun 2020 09:46:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.05_summits.bed INFO @ Tue, 16 Jun 2020 09:46:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1013 records, 4 fields): 3 millis INFO @ Tue, 16 Jun 2020 09:46:39: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 09:46:39: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 09:46:39: #1 total tags in treatment: 18348834 INFO @ Tue, 16 Jun 2020 09:46:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:46:39: #1 tags after filtering in treatment: 18348834 INFO @ Tue, 16 Jun 2020 09:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:46:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:46:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:46:40: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 09:46:40: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 09:46:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:46:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:46:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:46:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:46:40: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:46:40: #2 alternative fragment length(s) may be 2,52 bps INFO @ Tue, 16 Jun 2020 09:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.20_model.r WARNING @ Tue, 16 Jun 2020 09:46:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:46:40: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Tue, 16 Jun 2020 09:46:40: #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 09:46:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:46:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.10_summits.bed INFO @ Tue, 16 Jun 2020 09:47:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (476 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:47:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4344426/SRX4344426.20_summits.bed INFO @ Tue, 16 Jun 2020 09:47:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling