Job ID = 6367232 SRX = SRX3043418 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:20:01 prefetch.2.10.7: 1) Downloading 'SRR5875902'... 2020-06-15T23:20:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:57 prefetch.2.10.7: 1) 'SRR5875902' was downloaded successfully 2020-06-15T23:21:57 prefetch.2.10.7: 'SRR5875902' has 0 unresolved dependencies Read 25911671 spots for SRR5875902/SRR5875902.sra Written 25911671 spots for SRR5875902/SRR5875902.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: 00:08:16 25911671 reads; of these: 25911671 (100.00%) were unpaired; of these: 1708272 (6.59%) aligned 0 times 21706437 (83.77%) aligned exactly 1 time 2496962 (9.64%) aligned >1 times 93.41% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 5441169 / 24203399 = 0.2248 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 08:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.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 08:38:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:29: 1000000 INFO @ Tue, 16 Jun 2020 08:38:36: 2000000 INFO @ Tue, 16 Jun 2020 08:38:43: 3000000 INFO @ Tue, 16 Jun 2020 08:38:50: 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 08:38:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.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 08:38:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:57: 5000000 INFO @ Tue, 16 Jun 2020 08:39:00: 1000000 INFO @ Tue, 16 Jun 2020 08:39:04: 6000000 INFO @ Tue, 16 Jun 2020 08:39:08: 2000000 INFO @ Tue, 16 Jun 2020 08:39:12: 7000000 INFO @ Tue, 16 Jun 2020 08:39:15: 3000000 INFO @ Tue, 16 Jun 2020 08:39:19: 8000000 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 08:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.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 08:39:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:23: 4000000 INFO @ Tue, 16 Jun 2020 08:39:26: 9000000 INFO @ Tue, 16 Jun 2020 08:39:29: 1000000 INFO @ Tue, 16 Jun 2020 08:39:31: 5000000 INFO @ Tue, 16 Jun 2020 08:39:34: 10000000 INFO @ Tue, 16 Jun 2020 08:39:36: 2000000 INFO @ Tue, 16 Jun 2020 08:39:40: 6000000 INFO @ Tue, 16 Jun 2020 08:39:41: 11000000 INFO @ Tue, 16 Jun 2020 08:39:43: 3000000 INFO @ Tue, 16 Jun 2020 08:39:48: 7000000 INFO @ Tue, 16 Jun 2020 08:39:49: 12000000 INFO @ Tue, 16 Jun 2020 08:39:50: 4000000 INFO @ Tue, 16 Jun 2020 08:39:56: 8000000 INFO @ Tue, 16 Jun 2020 08:39:56: 13000000 INFO @ Tue, 16 Jun 2020 08:39:57: 5000000 INFO @ Tue, 16 Jun 2020 08:40:04: 6000000 INFO @ Tue, 16 Jun 2020 08:40:04: 9000000 INFO @ Tue, 16 Jun 2020 08:40:04: 14000000 INFO @ Tue, 16 Jun 2020 08:40:10: 7000000 INFO @ Tue, 16 Jun 2020 08:40:11: 15000000 INFO @ Tue, 16 Jun 2020 08:40:12: 10000000 INFO @ Tue, 16 Jun 2020 08:40:17: 8000000 INFO @ Tue, 16 Jun 2020 08:40:18: 16000000 INFO @ Tue, 16 Jun 2020 08:40:19: 11000000 INFO @ Tue, 16 Jun 2020 08:40:24: 9000000 INFO @ Tue, 16 Jun 2020 08:40:26: 17000000 INFO @ Tue, 16 Jun 2020 08:40:27: 12000000 INFO @ Tue, 16 Jun 2020 08:40:30: 10000000 INFO @ Tue, 16 Jun 2020 08:40:33: 18000000 INFO @ Tue, 16 Jun 2020 08:40:34: 13000000 INFO @ Tue, 16 Jun 2020 08:40:37: 11000000 INFO @ Tue, 16 Jun 2020 08:40:38: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:40:38: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:40:38: #1 total tags in treatment: 18762230 INFO @ Tue, 16 Jun 2020 08:40:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:38: #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 08:40:39: #1 tags after filtering in treatment: 18762230 INFO @ Tue, 16 Jun 2020 08:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:40: #2 number of paired peaks: 3043 INFO @ Tue, 16 Jun 2020 08:40:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:40: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:40:40: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 16 Jun 2020 08:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.05_model.r WARNING @ Tue, 16 Jun 2020 08:40:40: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:40: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 16 Jun 2020 08:40:40: #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 08:40:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:41: 14000000 INFO @ Tue, 16 Jun 2020 08:40:43: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:49: 15000000 INFO @ Tue, 16 Jun 2020 08:40:50: 13000000 INFO @ Tue, 16 Jun 2020 08:40:56: 16000000 INFO @ Tue, 16 Jun 2020 08:40:57: 14000000 INFO @ Tue, 16 Jun 2020 08:41:03: 17000000 INFO @ Tue, 16 Jun 2020 08:41:03: 15000000 INFO @ Tue, 16 Jun 2020 08:41:10: 16000000 INFO @ Tue, 16 Jun 2020 08:41:10: 18000000 INFO @ Tue, 16 Jun 2020 08:41:16: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:41:16: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:41:16: #1 total tags in treatment: 18762230 INFO @ Tue, 16 Jun 2020 08:41:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:16: #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 08:41:16: #1 tags after filtering in treatment: 18762230 INFO @ Tue, 16 Jun 2020 08:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:16: 17000000 INFO @ Tue, 16 Jun 2020 08:41:17: #2 number of paired peaks: 3043 INFO @ Tue, 16 Jun 2020 08:41:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:18: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:41:18: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 16 Jun 2020 08:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.10_model.r WARNING @ Tue, 16 Jun 2020 08:41:18: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:18: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 16 Jun 2020 08:41:18: #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 08:41:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:22: 18000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:27: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:41:27: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:41:27: #1 total tags in treatment: 18762230 INFO @ Tue, 16 Jun 2020 08:41:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:27: #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 08:41:27: #1 tags after filtering in treatment: 18762230 INFO @ Tue, 16 Jun 2020 08:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:29: #2 number of paired peaks: 3043 INFO @ Tue, 16 Jun 2020 08:41:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:29: #2 predicted fragment length is 95 bps INFO @ Tue, 16 Jun 2020 08:41:29: #2 alternative fragment length(s) may be 4,95 bps INFO @ Tue, 16 Jun 2020 08:41:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.20_model.r WARNING @ Tue, 16 Jun 2020 08:41:29: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:29: #2 You may need to consider one of the other alternative d(s): 4,95 WARNING @ Tue, 16 Jun 2020 08:41:29: #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 08:41:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6563 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4802 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043418/SRX3043418.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3567 records, 4 fields): 5 millis CompletedMACS2peakCalling