Job ID = 6369037 SRX = SRX982101 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:44 prefetch.2.10.7: 1) Downloading 'SRR1956588'... 2020-06-16T00:40:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:51 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:52 prefetch.2.10.7: 'SRR1956588' is valid 2020-06-16T00:41:52 prefetch.2.10.7: 1) 'SRR1956588' was downloaded successfully Read 8052112 spots for SRR1956588/SRR1956588.sra Written 8052112 spots for SRR1956588/SRR1956588.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: 00:01:51 8052112 reads; of these: 8052112 (100.00%) were unpaired; of these: 225704 (2.80%) aligned 0 times 6596024 (81.92%) aligned exactly 1 time 1230384 (15.28%) aligned >1 times 97.20% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 459421 / 7826408 = 0.0587 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 09:47:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.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 09:47:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:22: 1000000 INFO @ Tue, 16 Jun 2020 09:47:29: 2000000 INFO @ Tue, 16 Jun 2020 09:47:36: 3000000 INFO @ Tue, 16 Jun 2020 09:47:43: 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 @ Tue, 16 Jun 2020 09:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.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 09:47:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:51: 5000000 INFO @ Tue, 16 Jun 2020 09:47:54: 1000000 INFO @ Tue, 16 Jun 2020 09:47:58: 6000000 INFO @ Tue, 16 Jun 2020 09:48:02: 2000000 INFO @ Tue, 16 Jun 2020 09:48:05: 7000000 INFO @ Tue, 16 Jun 2020 09:48:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:08: #1 total tags in treatment: 7366987 INFO @ Tue, 16 Jun 2020 09:48:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:08: #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 09:48:08: #1 tags after filtering in treatment: 7366987 INFO @ Tue, 16 Jun 2020 09:48:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:09: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:48:09: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:09: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:48:09: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 09:48:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:09: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 09:48:09: #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 09:48:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:10: 3000000 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 09:48:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.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 09:48:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:17: 4000000 INFO @ Tue, 16 Jun 2020 09:48:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:24: 1000000 INFO @ Tue, 16 Jun 2020 09:48:25: 5000000 INFO @ Tue, 16 Jun 2020 09:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.05_summits.bed INFO @ Tue, 16 Jun 2020 09:48:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (506 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:32: 2000000 INFO @ Tue, 16 Jun 2020 09:48:32: 6000000 INFO @ Tue, 16 Jun 2020 09:48:39: 3000000 INFO @ Tue, 16 Jun 2020 09:48:40: 7000000 INFO @ Tue, 16 Jun 2020 09:48:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:43: #1 total tags in treatment: 7366987 INFO @ Tue, 16 Jun 2020 09:48:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:43: #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 09:48:43: #1 tags after filtering in treatment: 7366987 INFO @ Tue, 16 Jun 2020 09:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:43: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:48:43: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:43: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:48:43: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 09:48:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.10_model.r WARNING @ Tue, 16 Jun 2020 09:48:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:43: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 09:48:43: #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 09:48:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:47: 4000000 INFO @ Tue, 16 Jun 2020 09:48:54: 5000000 INFO @ Tue, 16 Jun 2020 09:48:57: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:02: 6000000 INFO @ Tue, 16 Jun 2020 09:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:09: 7000000 INFO @ Tue, 16 Jun 2020 09:49:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:12: #1 total tags in treatment: 7366987 INFO @ Tue, 16 Jun 2020 09:49:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:12: #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 09:49:12: #1 tags after filtering in treatment: 7366987 INFO @ Tue, 16 Jun 2020 09:49:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:12: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:49:12: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:12: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:49:12: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 09:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:12: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 09:49:12: #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 09:49:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982101/SRX982101.20_summits.bed INFO @ Tue, 16 Jun 2020 09:49:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 2 millis CompletedMACS2peakCalling