Job ID = 6369042 SRX = SRX982106 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:42:42 prefetch.2.10.7: 1) Downloading 'SRR1956595'... 2020-06-16T00:42:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:43:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:43:33 prefetch.2.10.7: 'SRR1956595' is valid 2020-06-16T00:43:33 prefetch.2.10.7: 1) 'SRR1956595' was downloaded successfully Read 5368560 spots for SRR1956595/SRR1956595.sra Written 5368560 spots for SRR1956595/SRR1956595.sra 2020-06-16T00:44:00 prefetch.2.10.7: 1) Downloading 'SRR1956596'... 2020-06-16T00:44:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:45 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:45 prefetch.2.10.7: 'SRR1956596' is valid 2020-06-16T00:45:45 prefetch.2.10.7: 1) 'SRR1956596' was downloaded successfully Read 6347799 spots for SRR1956596/SRR1956596.sra Written 6347799 spots for SRR1956596/SRR1956596.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: 00:02:30 11716359 reads; of these: 11716359 (100.00%) were unpaired; of these: 1286759 (10.98%) aligned 0 times 8734201 (74.55%) aligned exactly 1 time 1695399 (14.47%) aligned >1 times 89.02% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 818499 / 10429600 = 0.0785 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 09:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.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 09:52:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:18: 1000000 INFO @ Tue, 16 Jun 2020 09:52:23: 2000000 INFO @ Tue, 16 Jun 2020 09:52:29: 3000000 INFO @ Tue, 16 Jun 2020 09:52:34: 4000000 INFO @ Tue, 16 Jun 2020 09:52:40: 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 09:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.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 09:52:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:46: 6000000 INFO @ Tue, 16 Jun 2020 09:52:48: 1000000 INFO @ Tue, 16 Jun 2020 09:52:52: 7000000 INFO @ Tue, 16 Jun 2020 09:52:54: 2000000 INFO @ Tue, 16 Jun 2020 09:52:58: 8000000 INFO @ Tue, 16 Jun 2020 09:53:01: 3000000 INFO @ Tue, 16 Jun 2020 09:53:05: 9000000 INFO @ Tue, 16 Jun 2020 09:53:07: 4000000 INFO @ Tue, 16 Jun 2020 09:53:09: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:53:09: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:53:09: #1 total tags in treatment: 9611101 INFO @ Tue, 16 Jun 2020 09:53:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:09: #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 09:53:09: #1 tags after filtering in treatment: 9611101 INFO @ Tue, 16 Jun 2020 09:53:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:09: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 09:53:09: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:10: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:53:10: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.05_model.r WARNING @ Tue, 16 Jun 2020 09:53:10: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:10: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:53:10: #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 09:53:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:10: #3 Pre-compute pvalue-qvalue table... 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 09:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.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 09:53:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:13: 5000000 INFO @ Tue, 16 Jun 2020 09:53:19: 1000000 INFO @ Tue, 16 Jun 2020 09:53:20: 6000000 INFO @ Tue, 16 Jun 2020 09:53:26: 2000000 INFO @ Tue, 16 Jun 2020 09:53:26: 7000000 INFO @ Tue, 16 Jun 2020 09:53:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:33: 8000000 INFO @ Tue, 16 Jun 2020 09:53:33: 3000000 INFO @ Tue, 16 Jun 2020 09:53:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (589 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:39: 9000000 INFO @ Tue, 16 Jun 2020 09:53:41: 4000000 INFO @ Tue, 16 Jun 2020 09:53:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:53:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:53:43: #1 total tags in treatment: 9611101 INFO @ Tue, 16 Jun 2020 09:53:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:43: #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 09:53:44: #1 tags after filtering in treatment: 9611101 INFO @ Tue, 16 Jun 2020 09:53:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:44: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 09:53:44: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:44: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:53:44: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:53:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.10_model.r WARNING @ Tue, 16 Jun 2020 09:53:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:44: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:53:44: #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 09:53:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:48: 5000000 INFO @ Tue, 16 Jun 2020 09:53:54: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:01: 7000000 INFO @ Tue, 16 Jun 2020 09:54:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:07: 8000000 INFO @ Tue, 16 Jun 2020 09:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:13: 9000000 INFO @ Tue, 16 Jun 2020 09:54:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:17: #1 total tags in treatment: 9611101 INFO @ Tue, 16 Jun 2020 09:54:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:17: #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 09:54:17: #1 tags after filtering in treatment: 9611101 INFO @ Tue, 16 Jun 2020 09:54:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:18: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 09:54:18: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:18: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:54:18: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 16 Jun 2020 09:54:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.20_model.r WARNING @ Tue, 16 Jun 2020 09:54:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:18: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 16 Jun 2020 09:54:18: #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 09:54:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982106/SRX982106.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 1 millis CompletedMACS2peakCalling