Job ID = 6368484 SRX = SRX5020714 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:10 prefetch.2.10.7: 1) Downloading 'SRR8201337'... 2020-06-16T00:17:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:18:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:18:56 prefetch.2.10.7: 'SRR8201337' is valid 2020-06-16T00:18:56 prefetch.2.10.7: 1) 'SRR8201337' was downloaded successfully Read 10412425 spots for SRR8201337/SRR8201337.sra Written 10412425 spots for SRR8201337/SRR8201337.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: 00:02:25 10412425 reads; of these: 10412425 (100.00%) were unpaired; of these: 183949 (1.77%) aligned 0 times 8344251 (80.14%) aligned exactly 1 time 1884225 (18.10%) aligned >1 times 98.23% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 686635 / 10228476 = 0.0671 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 09:24:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.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 09:24:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:02: 1000000 INFO @ Tue, 16 Jun 2020 09:25:07: 2000000 INFO @ Tue, 16 Jun 2020 09:25:13: 3000000 INFO @ Tue, 16 Jun 2020 09:25:18: 4000000 INFO @ Tue, 16 Jun 2020 09:25:23: 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 09:25:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.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 09:25:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:29: 6000000 INFO @ Tue, 16 Jun 2020 09:25:32: 1000000 INFO @ Tue, 16 Jun 2020 09:25:35: 7000000 INFO @ Tue, 16 Jun 2020 09:25:38: 2000000 INFO @ Tue, 16 Jun 2020 09:25:41: 8000000 INFO @ Tue, 16 Jun 2020 09:25:44: 3000000 INFO @ Tue, 16 Jun 2020 09:25:46: 9000000 INFO @ Tue, 16 Jun 2020 09:25:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:25:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:25:49: #1 total tags in treatment: 9541841 INFO @ Tue, 16 Jun 2020 09:25:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:49: #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 09:25:50: 4000000 INFO @ Tue, 16 Jun 2020 09:25:50: #1 tags after filtering in treatment: 9541841 INFO @ Tue, 16 Jun 2020 09:25:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:50: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 09:25:50: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:50: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:25:50: #2 alternative fragment length(s) may be 3,49,557 bps INFO @ Tue, 16 Jun 2020 09:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:50: #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 09:25:50: #2 You may need to consider one of the other alternative d(s): 3,49,557 WARNING @ Tue, 16 Jun 2020 09:25:50: #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 09:25:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:50: #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 09:25:55: 5000000 INFO @ Tue, 16 Jun 2020 09:25:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.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 09:25:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:01: 6000000 INFO @ Tue, 16 Jun 2020 09:26:02: 1000000 INFO @ Tue, 16 Jun 2020 09:26:07: 7000000 INFO @ Tue, 16 Jun 2020 09:26:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:08: 2000000 INFO @ Tue, 16 Jun 2020 09:26:12: 8000000 INFO @ Tue, 16 Jun 2020 09:26:14: 3000000 INFO @ Tue, 16 Jun 2020 09:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (688 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:18: 9000000 INFO @ Tue, 16 Jun 2020 09:26:20: 4000000 INFO @ Tue, 16 Jun 2020 09:26:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:21: #1 total tags in treatment: 9541841 INFO @ Tue, 16 Jun 2020 09:26:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:21: #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 09:26:21: #1 tags after filtering in treatment: 9541841 INFO @ Tue, 16 Jun 2020 09:26:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:22: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 09:26:22: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:22: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:26:22: #2 alternative fragment length(s) may be 3,49,557 bps INFO @ Tue, 16 Jun 2020 09:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:22: #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 09:26:22: #2 You may need to consider one of the other alternative d(s): 3,49,557 WARNING @ Tue, 16 Jun 2020 09:26:22: #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 09:26:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:25: 5000000 INFO @ Tue, 16 Jun 2020 09:26:31: 6000000 INFO @ Tue, 16 Jun 2020 09:26:36: 7000000 INFO @ Tue, 16 Jun 2020 09:26:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:47: 9000000 INFO @ Tue, 16 Jun 2020 09:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (432 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:51: #1 total tags in treatment: 9541841 INFO @ Tue, 16 Jun 2020 09:26:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:51: #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 09:26:51: #1 tags after filtering in treatment: 9541841 INFO @ Tue, 16 Jun 2020 09:26:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:51: #2 number of paired peaks: 335 WARNING @ Tue, 16 Jun 2020 09:26:51: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:51: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:26:51: #2 alternative fragment length(s) may be 3,49,557 bps INFO @ Tue, 16 Jun 2020 09:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.20_model.r WARNING @ Tue, 16 Jun 2020 09:26:51: #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 09:26:51: #2 You may need to consider one of the other alternative d(s): 3,49,557 WARNING @ Tue, 16 Jun 2020 09:26:51: #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 09:26:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020714/SRX5020714.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (202 records, 4 fields): 1 millis CompletedMACS2peakCalling