Job ID = 6367177 SRX = SRX2973383 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:46 prefetch.2.10.7: 1) Downloading 'SRR5786986'... 2020-06-15T23:10:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:57 prefetch.2.10.7: 1) 'SRR5786986' was downloaded successfully Read 24188927 spots for SRR5786986/SRR5786986.sra Written 24188927 spots for SRR5786986/SRR5786986.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: 00:11:08 24188927 reads; of these: 24188927 (100.00%) were unpaired; of these: 1135558 (4.69%) aligned 0 times 19858382 (82.10%) aligned exactly 1 time 3194987 (13.21%) aligned >1 times 95.31% overall alignment rate Time searching: 00:11:08 Overall time: 00:11:08 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] 4341347 / 23053369 = 0.1883 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 08:33:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.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 08:33:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:33:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:33:52: 1000000 INFO @ Tue, 16 Jun 2020 08:33:59: 2000000 INFO @ Tue, 16 Jun 2020 08:34:07: 3000000 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 08:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.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 08:34:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:14: 4000000 INFO @ Tue, 16 Jun 2020 08:34:22: 1000000 INFO @ Tue, 16 Jun 2020 08:34:22: 5000000 INFO @ Tue, 16 Jun 2020 08:34:30: 2000000 INFO @ Tue, 16 Jun 2020 08:34:30: 6000000 INFO @ Tue, 16 Jun 2020 08:34:38: 3000000 INFO @ Tue, 16 Jun 2020 08:34:38: 7000000 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 08:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.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 08:34:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:46: 4000000 INFO @ Tue, 16 Jun 2020 08:34:46: 8000000 INFO @ Tue, 16 Jun 2020 08:34:51: 1000000 INFO @ Tue, 16 Jun 2020 08:34:54: 5000000 INFO @ Tue, 16 Jun 2020 08:34:54: 9000000 INFO @ Tue, 16 Jun 2020 08:34:58: 2000000 INFO @ Tue, 16 Jun 2020 08:35:01: 6000000 INFO @ Tue, 16 Jun 2020 08:35:02: 10000000 INFO @ Tue, 16 Jun 2020 08:35:05: 3000000 INFO @ Tue, 16 Jun 2020 08:35:09: 7000000 INFO @ Tue, 16 Jun 2020 08:35:10: 11000000 INFO @ Tue, 16 Jun 2020 08:35:11: 4000000 INFO @ Tue, 16 Jun 2020 08:35:17: 8000000 INFO @ Tue, 16 Jun 2020 08:35:18: 12000000 INFO @ Tue, 16 Jun 2020 08:35:18: 5000000 INFO @ Tue, 16 Jun 2020 08:35:25: 6000000 INFO @ Tue, 16 Jun 2020 08:35:25: 9000000 INFO @ Tue, 16 Jun 2020 08:35:26: 13000000 INFO @ Tue, 16 Jun 2020 08:35:32: 7000000 INFO @ Tue, 16 Jun 2020 08:35:33: 10000000 INFO @ Tue, 16 Jun 2020 08:35:34: 14000000 INFO @ Tue, 16 Jun 2020 08:35:39: 8000000 INFO @ Tue, 16 Jun 2020 08:35:41: 11000000 INFO @ Tue, 16 Jun 2020 08:35:42: 15000000 INFO @ Tue, 16 Jun 2020 08:35:45: 9000000 INFO @ Tue, 16 Jun 2020 08:35:49: 12000000 INFO @ Tue, 16 Jun 2020 08:35:50: 16000000 INFO @ Tue, 16 Jun 2020 08:35:52: 10000000 INFO @ Tue, 16 Jun 2020 08:35:57: 13000000 INFO @ Tue, 16 Jun 2020 08:35:58: 17000000 INFO @ Tue, 16 Jun 2020 08:35:59: 11000000 INFO @ Tue, 16 Jun 2020 08:36:04: 14000000 INFO @ Tue, 16 Jun 2020 08:36:05: 12000000 INFO @ Tue, 16 Jun 2020 08:36:06: 18000000 INFO @ Tue, 16 Jun 2020 08:36:12: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:36:12: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:36:12: #1 total tags in treatment: 18712022 INFO @ Tue, 16 Jun 2020 08:36:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:12: #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 08:36:12: #1 tags after filtering in treatment: 18712022 INFO @ Tue, 16 Jun 2020 08:36:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:12: 15000000 INFO @ Tue, 16 Jun 2020 08:36:12: 13000000 INFO @ Tue, 16 Jun 2020 08:36:13: #2 number of paired peaks: 1738 INFO @ Tue, 16 Jun 2020 08:36:13: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:13: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:13: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:13: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:13: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 08:36:13: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 08:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:13: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:13: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Tue, 16 Jun 2020 08:36:13: #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 08:36:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:19: 14000000 INFO @ Tue, 16 Jun 2020 08:36:20: 16000000 INFO @ Tue, 16 Jun 2020 08:36:25: 15000000 INFO @ Tue, 16 Jun 2020 08:36:28: 17000000 INFO @ Tue, 16 Jun 2020 08:36:32: 16000000 INFO @ Tue, 16 Jun 2020 08:36:36: 18000000 INFO @ Tue, 16 Jun 2020 08:36:39: 17000000 INFO @ Tue, 16 Jun 2020 08:36:41: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:36:41: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:36:41: #1 total tags in treatment: 18712022 INFO @ Tue, 16 Jun 2020 08:36:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:41: #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 08:36:41: #1 tags after filtering in treatment: 18712022 INFO @ Tue, 16 Jun 2020 08:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:43: #2 number of paired peaks: 1738 INFO @ Tue, 16 Jun 2020 08:36:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:43: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 08:36:43: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 08:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.10_model.r WARNING @ Tue, 16 Jun 2020 08:36:43: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:43: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Tue, 16 Jun 2020 08:36:43: #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 08:36:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:45: 18000000 INFO @ Tue, 16 Jun 2020 08:36:50: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:36:50: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:36:50: #1 total tags in treatment: 18712022 INFO @ Tue, 16 Jun 2020 08:36:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:50: #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 08:36:50: #1 tags after filtering in treatment: 18712022 INFO @ Tue, 16 Jun 2020 08:36:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:52: #2 number of paired peaks: 1738 INFO @ Tue, 16 Jun 2020 08:36:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:52: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 08:36:52: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 08:36:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.20_model.r WARNING @ Tue, 16 Jun 2020 08:36:52: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:36:52: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Tue, 16 Jun 2020 08:36:52: #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 08:36:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:36:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5429 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4254 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2973383/SRX2973383.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3124 records, 4 fields): 5 millis CompletedMACS2peakCalling