Job ID = 6365828 SRX = ERX1999199 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:24:14 prefetch.2.10.7: 1) Downloading 'ERR1938666'... 2020-06-15T22:24:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:25:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:25:13 prefetch.2.10.7: 'ERR1938666' is valid 2020-06-15T22:25:14 prefetch.2.10.7: 1) 'ERR1938666' was downloaded successfully Read 11243482 spots for ERR1938666/ERR1938666.sra Written 11243482 spots for ERR1938666/ERR1938666.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: 00:00:01 Multiseed full-index search: 00:02:57 11243482 reads; of these: 11243482 (100.00%) were unpaired; of these: 171036 (1.52%) aligned 0 times 8110117 (72.13%) aligned exactly 1 time 2962329 (26.35%) aligned >1 times 98.48% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 3778688 / 11072446 = 0.3413 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 07:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.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 07:31:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:31:34: 1000000 INFO @ Tue, 16 Jun 2020 07:31:40: 2000000 INFO @ Tue, 16 Jun 2020 07:31:46: 3000000 INFO @ Tue, 16 Jun 2020 07:31:52: 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 07:31:58: 5000000 INFO @ Tue, 16 Jun 2020 07:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.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 07:31:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:31:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:04: 6000000 INFO @ Tue, 16 Jun 2020 07:32:05: 1000000 INFO @ Tue, 16 Jun 2020 07:32:11: 7000000 INFO @ Tue, 16 Jun 2020 07:32:12: 2000000 INFO @ Tue, 16 Jun 2020 07:32:13: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:32:13: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:32:13: #1 total tags in treatment: 7293758 INFO @ Tue, 16 Jun 2020 07:32:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:13: #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 07:32:13: #1 tags after filtering in treatment: 7293758 INFO @ Tue, 16 Jun 2020 07:32:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:14: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 07:32:14: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 07:32:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:14: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:32:14: #2 alternative fragment length(s) may be 3,39,596 bps INFO @ Tue, 16 Jun 2020 07:32:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.05_model.r WARNING @ Tue, 16 Jun 2020 07:32:14: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:32:14: #2 You may need to consider one of the other alternative d(s): 3,39,596 WARNING @ Tue, 16 Jun 2020 07:32:14: #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 07:32:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:18: 3000000 INFO @ Tue, 16 Jun 2020 07:32:24: 4000000 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 07:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.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 07:32:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:32:30: 5000000 INFO @ Tue, 16 Jun 2020 07:32:36: 1000000 INFO @ Tue, 16 Jun 2020 07:32:37: 6000000 INFO @ Tue, 16 Jun 2020 07:32:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:32:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:32:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.05_summits.bed INFO @ Tue, 16 Jun 2020 07:32:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:32:44: 2000000 INFO @ Tue, 16 Jun 2020 07:32:44: 7000000 INFO @ Tue, 16 Jun 2020 07:32:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:32:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:32:46: #1 total tags in treatment: 7293758 INFO @ Tue, 16 Jun 2020 07:32:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:46: #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 07:32:46: #1 tags after filtering in treatment: 7293758 INFO @ Tue, 16 Jun 2020 07:32:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:46: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:47: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 07:32:47: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 07:32:47: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:47: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:47: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:47: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:47: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:32:47: #2 alternative fragment length(s) may be 3,39,596 bps INFO @ Tue, 16 Jun 2020 07:32:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.10_model.r WARNING @ Tue, 16 Jun 2020 07:32:47: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:32:47: #2 You may need to consider one of the other alternative d(s): 3,39,596 WARNING @ Tue, 16 Jun 2020 07:32:47: #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 07:32:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:51: 3000000 INFO @ Tue, 16 Jun 2020 07:32:58: 4000000 INFO @ Tue, 16 Jun 2020 07:33:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:05: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:33:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.10_summits.bed INFO @ Tue, 16 Jun 2020 07:33:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:33:12: 6000000 INFO @ Tue, 16 Jun 2020 07:33:19: 7000000 INFO @ Tue, 16 Jun 2020 07:33:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:33:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:33:21: #1 total tags in treatment: 7293758 INFO @ Tue, 16 Jun 2020 07:33:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:21: #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 07:33:21: #1 tags after filtering in treatment: 7293758 INFO @ Tue, 16 Jun 2020 07:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:21: #2 number of paired peaks: 381 WARNING @ Tue, 16 Jun 2020 07:33:21: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Tue, 16 Jun 2020 07:33:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:21: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:33:21: #2 alternative fragment length(s) may be 3,39,596 bps INFO @ Tue, 16 Jun 2020 07:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.20_model.r WARNING @ Tue, 16 Jun 2020 07:33:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:33:21: #2 You may need to consider one of the other alternative d(s): 3,39,596 WARNING @ Tue, 16 Jun 2020 07:33:21: #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 07:33:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:33:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/ERX1999199/ERX1999199.20_summits.bed INFO @ Tue, 16 Jun 2020 07:33:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (50 records, 4 fields): 1 millis CompletedMACS2peakCalling