Job ID = 6368038 SRX = SRX466501 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:48:18 prefetch.2.10.7: 1) Downloading 'SRR1163567'... 2020-06-15T23:48:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:23 prefetch.2.10.7: 1) 'SRR1163567' was downloaded successfully Read 15082416 spots for SRR1163567/SRR1163567.sra Written 15082416 spots for SRR1163567/SRR1163567.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: 00:02:49 15082416 reads; of these: 15082416 (100.00%) were unpaired; of these: 734166 (4.87%) aligned 0 times 12499104 (82.87%) aligned exactly 1 time 1849146 (12.26%) aligned >1 times 95.13% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 4299973 / 14348250 = 0.2997 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 08:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.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 08:58:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:36: 1000000 INFO @ Tue, 16 Jun 2020 08:58:41: 2000000 INFO @ Tue, 16 Jun 2020 08:58:46: 3000000 INFO @ Tue, 16 Jun 2020 08:58:51: 4000000 INFO @ Tue, 16 Jun 2020 08:58:56: 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 08:59:01: 6000000 INFO @ Tue, 16 Jun 2020 08:59:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.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 08:59:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:06: 7000000 INFO @ Tue, 16 Jun 2020 08:59:07: 1000000 INFO @ Tue, 16 Jun 2020 08:59:11: 8000000 INFO @ Tue, 16 Jun 2020 08:59:12: 2000000 INFO @ Tue, 16 Jun 2020 08:59:16: 9000000 INFO @ Tue, 16 Jun 2020 08:59:17: 3000000 INFO @ Tue, 16 Jun 2020 08:59:21: 10000000 INFO @ Tue, 16 Jun 2020 08:59:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:59:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:59:21: #1 total tags in treatment: 10048277 INFO @ Tue, 16 Jun 2020 08:59:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:21: #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 08:59:21: #1 tags after filtering in treatment: 10048277 INFO @ Tue, 16 Jun 2020 08:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:22: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 08:59:22: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:22: 4000000 INFO @ Tue, 16 Jun 2020 08:59:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:22: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:59:22: #2 alternative fragment length(s) may be 3,42,584 bps INFO @ Tue, 16 Jun 2020 08:59:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.05_model.r WARNING @ Tue, 16 Jun 2020 08:59:22: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:22: #2 You may need to consider one of the other alternative d(s): 3,42,584 WARNING @ Tue, 16 Jun 2020 08:59:22: #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 08:59:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:27: 5000000 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 08:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.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 08:59:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:32: 6000000 INFO @ Tue, 16 Jun 2020 08:59:37: 1000000 INFO @ Tue, 16 Jun 2020 08:59:37: 7000000 INFO @ Tue, 16 Jun 2020 08:59:42: 2000000 INFO @ Tue, 16 Jun 2020 08:59:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:42: 8000000 INFO @ Tue, 16 Jun 2020 08:59:47: 3000000 INFO @ Tue, 16 Jun 2020 08:59:47: 9000000 INFO @ Tue, 16 Jun 2020 08:59:52: 4000000 INFO @ Tue, 16 Jun 2020 08:59:53: 10000000 INFO @ Tue, 16 Jun 2020 08:59:53: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:59:53: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:59:53: #1 total tags in treatment: 10048277 INFO @ Tue, 16 Jun 2020 08:59:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:53: #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 08:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.05_summits.bed INFO @ Tue, 16 Jun 2020 08:59:53: Done! INFO @ Tue, 16 Jun 2020 08:59:53: #1 tags after filtering in treatment: 10048277 INFO @ Tue, 16 Jun 2020 08:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:53: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1457 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:59:54: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 08:59:54: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:54: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 08:59:54: #2 alternative fragment length(s) may be 3,42,584 bps INFO @ Tue, 16 Jun 2020 08:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.10_model.r WARNING @ Tue, 16 Jun 2020 08:59:54: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:54: #2 You may need to consider one of the other alternative d(s): 3,42,584 WARNING @ Tue, 16 Jun 2020 08:59:54: #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 08:59:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:58: 5000000 INFO @ Tue, 16 Jun 2020 09:00:03: 6000000 INFO @ Tue, 16 Jun 2020 09:00:08: 7000000 INFO @ Tue, 16 Jun 2020 09:00:12: 8000000 INFO @ Tue, 16 Jun 2020 09:00:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:17: 9000000 INFO @ Tue, 16 Jun 2020 09:00:22: 10000000 INFO @ Tue, 16 Jun 2020 09:00:23: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:00:23: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:00:23: #1 total tags in treatment: 10048277 INFO @ Tue, 16 Jun 2020 09:00:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:23: #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 09:00:23: #1 tags after filtering in treatment: 10048277 INFO @ Tue, 16 Jun 2020 09:00:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:23: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 09:00:23: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:23: Done! INFO @ Tue, 16 Jun 2020 09:00:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:23: #2 predicted fragment length is 42 bps INFO @ Tue, 16 Jun 2020 09:00:23: #2 alternative fragment length(s) may be 3,42,584 bps INFO @ Tue, 16 Jun 2020 09:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.20_model.r WARNING @ Tue, 16 Jun 2020 09:00:23: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:23: #2 You may need to consider one of the other alternative d(s): 3,42,584 WARNING @ Tue, 16 Jun 2020 09:00:23: #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 09:00:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:00:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466501/SRX466501.20_summits.bed INFO @ Tue, 16 Jun 2020 09:00:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 1 millis CompletedMACS2peakCalling