Job ID = 6507991 SRX = SRX743641 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:28:04 prefetch.2.10.7: 1) Downloading 'SRR1630856'... 2020-06-26T13:28:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:29:38 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:29:39 prefetch.2.10.7: 'SRR1630856' is valid 2020-06-26T13:29:39 prefetch.2.10.7: 1) 'SRR1630856' was downloaded successfully Read 13719552 spots for SRR1630856/SRR1630856.sra Written 13719552 spots for SRR1630856/SRR1630856.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:46 13719552 reads; of these: 13719552 (100.00%) were unpaired; of these: 3519983 (25.66%) aligned 0 times 9182177 (66.93%) aligned exactly 1 time 1017392 (7.42%) aligned >1 times 74.34% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 1372691 / 10199569 = 0.1346 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 22:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.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 22:36:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:36: 1000000 INFO @ Fri, 26 Jun 2020 22:36:42: 2000000 INFO @ Fri, 26 Jun 2020 22:36:47: 3000000 INFO @ Fri, 26 Jun 2020 22:36:52: 4000000 INFO @ Fri, 26 Jun 2020 22:36:58: 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 22:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.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 22:37:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:03: 6000000 INFO @ Fri, 26 Jun 2020 22:37:07: 1000000 INFO @ Fri, 26 Jun 2020 22:37:09: 7000000 INFO @ Fri, 26 Jun 2020 22:37:13: 2000000 INFO @ Fri, 26 Jun 2020 22:37:15: 8000000 INFO @ Fri, 26 Jun 2020 22:37:18: 3000000 INFO @ Fri, 26 Jun 2020 22:37:19: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:37:19: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:37:19: #1 total tags in treatment: 8826878 INFO @ Fri, 26 Jun 2020 22:37:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:19: #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 22:37:20: #1 tags after filtering in treatment: 8826878 INFO @ Fri, 26 Jun 2020 22:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:20: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:20: #2 number of paired peaks: 201 WARNING @ Fri, 26 Jun 2020 22:37:20: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:20: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:20: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 22:37:20: #2 alternative fragment length(s) may be 2,53,113,135,163,178,202,217,278,474 bps INFO @ Fri, 26 Jun 2020 22:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.05_model.r WARNING @ Fri, 26 Jun 2020 22:37:20: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:37:20: #2 You may need to consider one of the other alternative d(s): 2,53,113,135,163,178,202,217,278,474 WARNING @ Fri, 26 Jun 2020 22:37:20: #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 22:37:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:37:24: 4000000 INFO @ Fri, 26 Jun 2020 22:37:29: 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 @ Fri, 26 Jun 2020 22:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.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 22:37:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:35: 6000000 INFO @ Fri, 26 Jun 2020 22:37:37: 1000000 INFO @ Fri, 26 Jun 2020 22:37:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:37:41: 7000000 INFO @ Fri, 26 Jun 2020 22:37:43: 2000000 INFO @ Fri, 26 Jun 2020 22:37:47: 8000000 INFO @ Fri, 26 Jun 2020 22:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.05_summits.bed INFO @ Fri, 26 Jun 2020 22:37:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1171 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:37:49: 3000000 INFO @ Fri, 26 Jun 2020 22:37:52: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:37:52: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:37:52: #1 total tags in treatment: 8826878 INFO @ Fri, 26 Jun 2020 22:37:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:37:52: #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 22:37:52: #1 tags after filtering in treatment: 8826878 INFO @ Fri, 26 Jun 2020 22:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:37:52: #1 finished! INFO @ Fri, 26 Jun 2020 22:37:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:37:52: #2 number of paired peaks: 201 WARNING @ Fri, 26 Jun 2020 22:37:52: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Fri, 26 Jun 2020 22:37:52: start model_add_line... INFO @ Fri, 26 Jun 2020 22:37:52: start X-correlation... INFO @ Fri, 26 Jun 2020 22:37:52: end of X-cor INFO @ Fri, 26 Jun 2020 22:37:52: #2 finished! INFO @ Fri, 26 Jun 2020 22:37:52: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 22:37:52: #2 alternative fragment length(s) may be 2,53,113,135,163,178,202,217,278,474 bps INFO @ Fri, 26 Jun 2020 22:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.10_model.r WARNING @ Fri, 26 Jun 2020 22:37:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:37:52: #2 You may need to consider one of the other alternative d(s): 2,53,113,135,163,178,202,217,278,474 WARNING @ Fri, 26 Jun 2020 22:37:52: #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 22:37:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:37:54: 4000000 INFO @ Fri, 26 Jun 2020 22:38:00: 5000000 INFO @ Fri, 26 Jun 2020 22:38:06: 6000000 INFO @ Fri, 26 Jun 2020 22:38:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:11: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:38:17: 8000000 INFO @ Fri, 26 Jun 2020 22:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.10_summits.bed INFO @ Fri, 26 Jun 2020 22:38:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:38:22: #1 tag size is determined as 52 bps INFO @ Fri, 26 Jun 2020 22:38:22: #1 tag size = 52 INFO @ Fri, 26 Jun 2020 22:38:22: #1 total tags in treatment: 8826878 INFO @ Fri, 26 Jun 2020 22:38:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:22: #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 22:38:22: #1 tags after filtering in treatment: 8826878 INFO @ Fri, 26 Jun 2020 22:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:22: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:22: #2 number of paired peaks: 201 WARNING @ Fri, 26 Jun 2020 22:38:22: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:22: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:22: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:22: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:22: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:22: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 22:38:22: #2 alternative fragment length(s) may be 2,53,113,135,163,178,202,217,278,474 bps INFO @ Fri, 26 Jun 2020 22:38:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.20_model.r WARNING @ Fri, 26 Jun 2020 22:38:22: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:22: #2 You may need to consider one of the other alternative d(s): 2,53,113,135,163,178,202,217,278,474 WARNING @ Fri, 26 Jun 2020 22:38:22: #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 22:38:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:38:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:38:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:38:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX743641/SRX743641.20_summits.bed INFO @ Fri, 26 Jun 2020 22:38:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling