Job ID = 6368382 SRX = SRX495061 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:29:31 prefetch.2.10.7: 1) Downloading 'SRR1198593'... 2020-06-16T00:29:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:30 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:30 prefetch.2.10.7: 1) 'SRR1198593' was downloaded successfully Read 16047878 spots for SRR1198593/SRR1198593.sra Written 16047878 spots for SRR1198593/SRR1198593.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: 00:02:54 16047878 reads; of these: 16047878 (100.00%) were unpaired; of these: 1451119 (9.04%) aligned 0 times 12366202 (77.06%) aligned exactly 1 time 2230557 (13.90%) aligned >1 times 90.96% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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_rmdupse_core] 1646721 / 14596759 = 0.1128 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 09:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.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 09:39:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:56: 1000000 INFO @ Tue, 16 Jun 2020 09:40:02: 2000000 INFO @ Tue, 16 Jun 2020 09:40:07: 3000000 INFO @ Tue, 16 Jun 2020 09:40:12: 4000000 INFO @ Tue, 16 Jun 2020 09:40:18: 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 09:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.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 09:40:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:23: 6000000 INFO @ Tue, 16 Jun 2020 09:40:27: 1000000 INFO @ Tue, 16 Jun 2020 09:40:29: 7000000 INFO @ Tue, 16 Jun 2020 09:40:33: 2000000 INFO @ Tue, 16 Jun 2020 09:40:35: 8000000 INFO @ Tue, 16 Jun 2020 09:40:39: 3000000 INFO @ Tue, 16 Jun 2020 09:40:41: 9000000 INFO @ Tue, 16 Jun 2020 09:40:45: 4000000 INFO @ Tue, 16 Jun 2020 09:40:47: 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 09:40:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.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 09:40:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:51: 5000000 INFO @ Tue, 16 Jun 2020 09:40:53: 11000000 INFO @ Tue, 16 Jun 2020 09:40:58: 1000000 INFO @ Tue, 16 Jun 2020 09:40:58: 6000000 INFO @ Tue, 16 Jun 2020 09:41:00: 12000000 INFO @ Tue, 16 Jun 2020 09:41:05: 7000000 INFO @ Tue, 16 Jun 2020 09:41:05: 2000000 INFO @ Tue, 16 Jun 2020 09:41:07: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:41:07: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:41:07: #1 total tags in treatment: 12950038 INFO @ Tue, 16 Jun 2020 09:41:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:07: #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 09:41:07: #1 tags after filtering in treatment: 12950038 INFO @ Tue, 16 Jun 2020 09:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:08: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 09:41:08: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:08: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:41:08: #2 alternative fragment length(s) may be 1,41,574 bps INFO @ Tue, 16 Jun 2020 09:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:08: #2 You may need to consider one of the other alternative d(s): 1,41,574 WARNING @ Tue, 16 Jun 2020 09:41:08: #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 09:41:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:11: 8000000 INFO @ Tue, 16 Jun 2020 09:41:12: 3000000 INFO @ Tue, 16 Jun 2020 09:41:18: 9000000 INFO @ Tue, 16 Jun 2020 09:41:19: 4000000 INFO @ Tue, 16 Jun 2020 09:41:25: 10000000 INFO @ Tue, 16 Jun 2020 09:41:27: 5000000 INFO @ Tue, 16 Jun 2020 09:41:32: 11000000 INFO @ Tue, 16 Jun 2020 09:41:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:34: 6000000 INFO @ Tue, 16 Jun 2020 09:41:38: 12000000 INFO @ Tue, 16 Jun 2020 09:41:42: 7000000 INFO @ Tue, 16 Jun 2020 09:41:45: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:41:45: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:41:45: #1 total tags in treatment: 12950038 INFO @ Tue, 16 Jun 2020 09:41:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:45: #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 09:41:45: #1 tags after filtering in treatment: 12950038 INFO @ Tue, 16 Jun 2020 09:41:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:46: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 09:41:46: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:46: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:41:46: #2 alternative fragment length(s) may be 1,41,574 bps INFO @ Tue, 16 Jun 2020 09:41:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:46: #2 You may need to consider one of the other alternative d(s): 1,41,574 WARNING @ Tue, 16 Jun 2020 09:41:46: #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 09:41:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (630 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:48: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:55: 9000000 INFO @ Tue, 16 Jun 2020 09:42:02: 10000000 INFO @ Tue, 16 Jun 2020 09:42:08: 11000000 INFO @ Tue, 16 Jun 2020 09:42:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:15: 12000000 INFO @ Tue, 16 Jun 2020 09:42:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:42:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:42:21: #1 total tags in treatment: 12950038 INFO @ Tue, 16 Jun 2020 09:42:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:21: #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 09:42:21: #1 tags after filtering in treatment: 12950038 INFO @ Tue, 16 Jun 2020 09:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:22: #2 number of paired peaks: 268 WARNING @ Tue, 16 Jun 2020 09:42:22: Fewer paired peaks (268) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 268 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:22: #2 predicted fragment length is 41 bps INFO @ Tue, 16 Jun 2020 09:42:22: #2 alternative fragment length(s) may be 1,41,574 bps INFO @ Tue, 16 Jun 2020 09:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:22: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:22: #2 You may need to consider one of the other alternative d(s): 1,41,574 WARNING @ Tue, 16 Jun 2020 09:42:22: #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 09:42:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495061/SRX495061.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling