Job ID = 6507816 SRX = SRX494821 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:56:56 prefetch.2.10.7: 1) Downloading 'SRR1198353'... 2020-06-26T13:56:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:59:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:59:25 prefetch.2.10.7: 'SRR1198353' is valid 2020-06-26T13:59:25 prefetch.2.10.7: 1) 'SRR1198353' was downloaded successfully Read 16864948 spots for SRR1198353/SRR1198353.sra Written 16864948 spots for SRR1198353/SRR1198353.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: 00:03:26 16864948 reads; of these: 16864948 (100.00%) were unpaired; of these: 917380 (5.44%) aligned 0 times 13167344 (78.08%) aligned exactly 1 time 2780224 (16.49%) aligned >1 times 94.56% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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 8 files... [bam_rmdupse_core] 2596337 / 15947568 = 0.1628 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 23:07:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.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 23:07:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:07:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:07:51: 1000000 INFO @ Fri, 26 Jun 2020 23:07:57: 2000000 INFO @ Fri, 26 Jun 2020 23:08:03: 3000000 INFO @ Fri, 26 Jun 2020 23:08:09: 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 @ Fri, 26 Jun 2020 23:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.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 23:08:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:08:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:08:15: 5000000 INFO @ Fri, 26 Jun 2020 23:08:21: 1000000 INFO @ Fri, 26 Jun 2020 23:08:22: 6000000 INFO @ Fri, 26 Jun 2020 23:08:28: 2000000 INFO @ Fri, 26 Jun 2020 23:08:28: 7000000 INFO @ Fri, 26 Jun 2020 23:08:34: 3000000 INFO @ Fri, 26 Jun 2020 23:08:35: 8000000 INFO @ Fri, 26 Jun 2020 23:08:41: 4000000 INFO @ Fri, 26 Jun 2020 23:08:41: 9000000 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 23:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.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 23:08:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:08:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:08:47: 5000000 INFO @ Fri, 26 Jun 2020 23:08:48: 10000000 INFO @ Fri, 26 Jun 2020 23:08:51: 1000000 INFO @ Fri, 26 Jun 2020 23:08:54: 6000000 INFO @ Fri, 26 Jun 2020 23:08:54: 11000000 INFO @ Fri, 26 Jun 2020 23:08:58: 2000000 INFO @ Fri, 26 Jun 2020 23:09:01: 7000000 INFO @ Fri, 26 Jun 2020 23:09:01: 12000000 INFO @ Fri, 26 Jun 2020 23:09:05: 3000000 INFO @ Fri, 26 Jun 2020 23:09:07: 8000000 INFO @ Fri, 26 Jun 2020 23:09:07: 13000000 INFO @ Fri, 26 Jun 2020 23:09:10: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:09:10: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:09:10: #1 total tags in treatment: 13351231 INFO @ Fri, 26 Jun 2020 23:09:10: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:09:10: #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 23:09:10: #1 tags after filtering in treatment: 13351231 INFO @ Fri, 26 Jun 2020 23:09:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:09:10: #1 finished! INFO @ Fri, 26 Jun 2020 23:09:10: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:09:11: #2 number of paired peaks: 227 WARNING @ Fri, 26 Jun 2020 23:09:11: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Fri, 26 Jun 2020 23:09:11: start model_add_line... INFO @ Fri, 26 Jun 2020 23:09:11: start X-correlation... INFO @ Fri, 26 Jun 2020 23:09:11: end of X-cor INFO @ Fri, 26 Jun 2020 23:09:11: #2 finished! INFO @ Fri, 26 Jun 2020 23:09:11: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 23:09:11: #2 alternative fragment length(s) may be 4,64 bps INFO @ Fri, 26 Jun 2020 23:09:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.05_model.r WARNING @ Fri, 26 Jun 2020 23:09:11: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:09:11: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Fri, 26 Jun 2020 23:09:11: #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 23:09:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:09:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:09:11: 4000000 INFO @ Fri, 26 Jun 2020 23:09:14: 9000000 INFO @ Fri, 26 Jun 2020 23:09:18: 5000000 INFO @ Fri, 26 Jun 2020 23:09:20: 10000000 INFO @ Fri, 26 Jun 2020 23:09:25: 6000000 INFO @ Fri, 26 Jun 2020 23:09:27: 11000000 INFO @ Fri, 26 Jun 2020 23:09:31: 7000000 INFO @ Fri, 26 Jun 2020 23:09:33: 12000000 INFO @ Fri, 26 Jun 2020 23:09:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:09:38: 8000000 INFO @ Fri, 26 Jun 2020 23:09:40: 13000000 INFO @ Fri, 26 Jun 2020 23:09:42: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:09:42: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:09:42: #1 total tags in treatment: 13351231 INFO @ Fri, 26 Jun 2020 23:09:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:09:42: #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 23:09:42: #1 tags after filtering in treatment: 13351231 INFO @ Fri, 26 Jun 2020 23:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:09:42: #1 finished! INFO @ Fri, 26 Jun 2020 23:09:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:09:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:09:43: #2 number of paired peaks: 227 WARNING @ Fri, 26 Jun 2020 23:09:43: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Fri, 26 Jun 2020 23:09:43: start model_add_line... INFO @ Fri, 26 Jun 2020 23:09:43: start X-correlation... INFO @ Fri, 26 Jun 2020 23:09:43: end of X-cor INFO @ Fri, 26 Jun 2020 23:09:43: #2 finished! INFO @ Fri, 26 Jun 2020 23:09:43: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 23:09:43: #2 alternative fragment length(s) may be 4,64 bps INFO @ Fri, 26 Jun 2020 23:09:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.10_model.r WARNING @ Fri, 26 Jun 2020 23:09:43: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:09:43: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Fri, 26 Jun 2020 23:09:43: #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 23:09:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:09:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:09:44: 9000000 INFO @ Fri, 26 Jun 2020 23:09:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:09:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:09:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.05_summits.bed INFO @ Fri, 26 Jun 2020 23:09:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2765 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:09:50: 10000000 INFO @ Fri, 26 Jun 2020 23:09:57: 11000000 INFO @ Fri, 26 Jun 2020 23:10:03: 12000000 INFO @ Fri, 26 Jun 2020 23:10:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:10:09: 13000000 INFO @ Fri, 26 Jun 2020 23:10:11: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 23:10:11: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 23:10:11: #1 total tags in treatment: 13351231 INFO @ Fri, 26 Jun 2020 23:10:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:10:11: #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 23:10:11: #1 tags after filtering in treatment: 13351231 INFO @ Fri, 26 Jun 2020 23:10:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:10:11: #1 finished! INFO @ Fri, 26 Jun 2020 23:10:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:10:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:10:12: #2 number of paired peaks: 227 WARNING @ Fri, 26 Jun 2020 23:10:12: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Fri, 26 Jun 2020 23:10:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:10:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:10:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:10:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:10:12: #2 predicted fragment length is 64 bps INFO @ Fri, 26 Jun 2020 23:10:12: #2 alternative fragment length(s) may be 4,64 bps INFO @ Fri, 26 Jun 2020 23:10:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.20_model.r WARNING @ Fri, 26 Jun 2020 23:10:12: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:10:12: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Fri, 26 Jun 2020 23:10:12: #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 23:10:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:10:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.10_summits.bed INFO @ Fri, 26 Jun 2020 23:10:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1564 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:10:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494821/SRX494821.20_summits.bed INFO @ Fri, 26 Jun 2020 23:10:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (805 records, 4 fields): 2 millis CompletedMACS2peakCalling