Job ID = 6507862 SRX = SRX494943 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:01:56 prefetch.2.10.7: 1) Downloading 'SRR1198475'... 2020-06-26T13:01:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:03:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:03:50 prefetch.2.10.7: 1) 'SRR1198475' was downloaded successfully Read 23003577 spots for SRR1198475/SRR1198475.sra Written 23003577 spots for SRR1198475/SRR1198475.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: 00:05:13 23003577 reads; of these: 23003577 (100.00%) were unpaired; of these: 1606988 (6.99%) aligned 0 times 17616054 (76.58%) aligned exactly 1 time 3780535 (16.43%) aligned >1 times 93.01% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 13811204 / 21396589 = 0.6455 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 @ Fri, 26 Jun 2020 22:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.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 @ Fri, 26 Jun 2020 22:14:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:14:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:14:20: 1000000 INFO @ Fri, 26 Jun 2020 22:14:26: 2000000 INFO @ Fri, 26 Jun 2020 22:14:31: 3000000 INFO @ Fri, 26 Jun 2020 22:14:37: 4000000 INFO @ Fri, 26 Jun 2020 22:14:42: 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 @ Fri, 26 Jun 2020 22:14:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.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 @ Fri, 26 Jun 2020 22:14:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:14:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:14:48: 6000000 INFO @ Fri, 26 Jun 2020 22:14:51: 1000000 INFO @ Fri, 26 Jun 2020 22:14:54: 7000000 INFO @ Fri, 26 Jun 2020 22:14:57: 2000000 INFO @ Fri, 26 Jun 2020 22:14:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:14:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:14:57: #1 total tags in treatment: 7585385 INFO @ Fri, 26 Jun 2020 22:14:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:14:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:14:57: #1 tags after filtering in treatment: 7585385 INFO @ Fri, 26 Jun 2020 22:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:14:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:14:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:14:58: #2 number of paired peaks: 636 WARNING @ Fri, 26 Jun 2020 22:14:58: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Fri, 26 Jun 2020 22:14:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:14:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:14:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:14:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:14:58: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:14:58: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.05_model.r WARNING @ Fri, 26 Jun 2020 22:14:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:14:58: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:14:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:14:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:14:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:15:02: 3000000 INFO @ Fri, 26 Jun 2020 22:15:08: 4000000 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 @ Fri, 26 Jun 2020 22:15:13: 5000000 INFO @ Fri, 26 Jun 2020 22:15:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.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 @ Fri, 26 Jun 2020 22:15:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:15:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:15:19: 6000000 INFO @ Fri, 26 Jun 2020 22:15:21: 1000000 INFO @ Fri, 26 Jun 2020 22:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.05_summits.bed INFO @ Fri, 26 Jun 2020 22:15:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (835 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:15:25: 7000000 INFO @ Fri, 26 Jun 2020 22:15:27: 2000000 INFO @ Fri, 26 Jun 2020 22:15:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:15:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:15:28: #1 total tags in treatment: 7585385 INFO @ Fri, 26 Jun 2020 22:15:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:15:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:15:28: #1 tags after filtering in treatment: 7585385 INFO @ Fri, 26 Jun 2020 22:15:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:15:28: #1 finished! INFO @ Fri, 26 Jun 2020 22:15:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:15:29: #2 number of paired peaks: 636 WARNING @ Fri, 26 Jun 2020 22:15:29: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Fri, 26 Jun 2020 22:15:29: start model_add_line... INFO @ Fri, 26 Jun 2020 22:15:29: start X-correlation... INFO @ Fri, 26 Jun 2020 22:15:29: end of X-cor INFO @ Fri, 26 Jun 2020 22:15:29: #2 finished! INFO @ Fri, 26 Jun 2020 22:15:29: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:15:29: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:15:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.10_model.r WARNING @ Fri, 26 Jun 2020 22:15:29: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:15:29: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:15:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:15:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:15:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:15:32: 3000000 INFO @ Fri, 26 Jun 2020 22:15:38: 4000000 INFO @ Fri, 26 Jun 2020 22:15:43: 5000000 INFO @ Fri, 26 Jun 2020 22:15:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:15:49: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.10_summits.bed INFO @ Fri, 26 Jun 2020 22:15:54: Done! INFO @ Fri, 26 Jun 2020 22:15:54: 7000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (570 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:15:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:15:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:15:57: #1 total tags in treatment: 7585385 INFO @ Fri, 26 Jun 2020 22:15:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:15:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:15:57: #1 tags after filtering in treatment: 7585385 INFO @ Fri, 26 Jun 2020 22:15:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:15:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:15:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:15:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:15:58: #2 number of paired peaks: 636 WARNING @ Fri, 26 Jun 2020 22:15:58: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Fri, 26 Jun 2020 22:15:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:15:58: start X-correlation... INFO @ Fri, 26 Jun 2020 22:15:58: end of X-cor INFO @ Fri, 26 Jun 2020 22:15:58: #2 finished! INFO @ Fri, 26 Jun 2020 22:15:58: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:15:58: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.20_model.r WARNING @ Fri, 26 Jun 2020 22:15:58: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:15:58: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:15:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:15:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:15:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:16:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:16:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:16:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:16:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494943/SRX494943.20_summits.bed INFO @ Fri, 26 Jun 2020 22:16:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 1 millis CompletedMACS2peakCalling