Job ID = 6497436 SRX = SRX494934 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:40:53 prefetch.2.10.7: 1) Downloading 'SRR1198466'... 2020-06-25T21:40:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:43:19 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:43:19 prefetch.2.10.7: 1) 'SRR1198466' was downloaded successfully Read 26578904 spots for SRR1198466/SRR1198466.sra Written 26578904 spots for SRR1198466/SRR1198466.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: 00:05:31 26578904 reads; of these: 26578904 (100.00%) were unpaired; of these: 1725070 (6.49%) aligned 0 times 21431414 (80.63%) aligned exactly 1 time 3422420 (12.88%) aligned >1 times 93.51% overall alignment rate Time searching: 00:05:31 Overall time: 00:05:31 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 12 files... [bam_rmdupse_core] 13207899 / 24853834 = 0.5314 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 06:57:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.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 06:57:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:57:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:57:11: 1000000 INFO @ Fri, 26 Jun 2020 06:57:18: 2000000 INFO @ Fri, 26 Jun 2020 06:57:24: 3000000 INFO @ Fri, 26 Jun 2020 06:57:30: 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 @ Fri, 26 Jun 2020 06:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.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 06:57:35: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:57:35: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:57:36: 5000000 INFO @ Fri, 26 Jun 2020 06:57:42: 1000000 INFO @ Fri, 26 Jun 2020 06:57:43: 6000000 INFO @ Fri, 26 Jun 2020 06:57:48: 2000000 INFO @ Fri, 26 Jun 2020 06:57:50: 7000000 INFO @ Fri, 26 Jun 2020 06:57:55: 3000000 INFO @ Fri, 26 Jun 2020 06:57:57: 8000000 INFO @ Fri, 26 Jun 2020 06:58:01: 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 @ Fri, 26 Jun 2020 06:58:03: 9000000 INFO @ Fri, 26 Jun 2020 06:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.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 06:58:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:58:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:58:08: 5000000 INFO @ Fri, 26 Jun 2020 06:58:10: 10000000 INFO @ Fri, 26 Jun 2020 06:58:12: 1000000 INFO @ Fri, 26 Jun 2020 06:58:15: 6000000 INFO @ Fri, 26 Jun 2020 06:58:17: 11000000 INFO @ Fri, 26 Jun 2020 06:58:19: 2000000 INFO @ Fri, 26 Jun 2020 06:58:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:58:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:58:21: #1 total tags in treatment: 11645935 INFO @ Fri, 26 Jun 2020 06:58:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:58:21: #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 06:58:22: 7000000 INFO @ Fri, 26 Jun 2020 06:58:22: #1 tags after filtering in treatment: 11645935 INFO @ Fri, 26 Jun 2020 06:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:58:22: #1 finished! INFO @ Fri, 26 Jun 2020 06:58:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:58:22: #2 number of paired peaks: 306 WARNING @ Fri, 26 Jun 2020 06:58:22: 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 @ Fri, 26 Jun 2020 06:58:22: start model_add_line... INFO @ Fri, 26 Jun 2020 06:58:23: start X-correlation... INFO @ Fri, 26 Jun 2020 06:58:23: end of X-cor INFO @ Fri, 26 Jun 2020 06:58:23: #2 finished! INFO @ Fri, 26 Jun 2020 06:58:23: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 06:58:23: #2 alternative fragment length(s) may be 2,46,538 bps INFO @ Fri, 26 Jun 2020 06:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.05_model.r WARNING @ Fri, 26 Jun 2020 06:58:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:58:25: #2 You may need to consider one of the other alternative d(s): 2,46,538 WARNING @ Fri, 26 Jun 2020 06:58:25: #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 06:58:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:58:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:58:26: 3000000 INFO @ Fri, 26 Jun 2020 06:58:28: 8000000 INFO @ Fri, 26 Jun 2020 06:58:33: 4000000 INFO @ Fri, 26 Jun 2020 06:58:35: 9000000 INFO @ Fri, 26 Jun 2020 06:58:39: 5000000 INFO @ Fri, 26 Jun 2020 06:58:41: 10000000 INFO @ Fri, 26 Jun 2020 06:58:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:58:46: 6000000 INFO @ Fri, 26 Jun 2020 06:58:48: 11000000 INFO @ Fri, 26 Jun 2020 06:58:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:58:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:58:52: #1 total tags in treatment: 11645935 INFO @ Fri, 26 Jun 2020 06:58:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:58:52: #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 06:58:52: #1 tags after filtering in treatment: 11645935 INFO @ Fri, 26 Jun 2020 06:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:58:52: #1 finished! INFO @ Fri, 26 Jun 2020 06:58:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:58:52: 7000000 INFO @ Fri, 26 Jun 2020 06:58:53: #2 number of paired peaks: 306 WARNING @ Fri, 26 Jun 2020 06:58:53: 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 @ Fri, 26 Jun 2020 06:58:53: start model_add_line... INFO @ Fri, 26 Jun 2020 06:58:53: start X-correlation... INFO @ Fri, 26 Jun 2020 06:58:53: end of X-cor INFO @ Fri, 26 Jun 2020 06:58:53: #2 finished! INFO @ Fri, 26 Jun 2020 06:58:53: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 06:58:53: #2 alternative fragment length(s) may be 2,46,538 bps INFO @ Fri, 26 Jun 2020 06:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.10_model.r WARNING @ Fri, 26 Jun 2020 06:58:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:58:54: #2 You may need to consider one of the other alternative d(s): 2,46,538 WARNING @ Fri, 26 Jun 2020 06:58:54: #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 06:58:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:58:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:58:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.05_summits.bed INFO @ Fri, 26 Jun 2020 06:58:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:58:58: 8000000 INFO @ Fri, 26 Jun 2020 06:59:04: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:59:10: 10000000 INFO @ Fri, 26 Jun 2020 06:59:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:59:16: 11000000 INFO @ Fri, 26 Jun 2020 06:59:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 06:59:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 06:59:20: #1 total tags in treatment: 11645935 INFO @ Fri, 26 Jun 2020 06:59:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:59:20: #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 06:59:20: #1 tags after filtering in treatment: 11645935 INFO @ Fri, 26 Jun 2020 06:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:59:20: #1 finished! INFO @ Fri, 26 Jun 2020 06:59:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:59:21: #2 number of paired peaks: 306 WARNING @ Fri, 26 Jun 2020 06:59:21: 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 @ Fri, 26 Jun 2020 06:59:21: start model_add_line... INFO @ Fri, 26 Jun 2020 06:59:21: start X-correlation... INFO @ Fri, 26 Jun 2020 06:59:21: end of X-cor INFO @ Fri, 26 Jun 2020 06:59:21: #2 finished! INFO @ Fri, 26 Jun 2020 06:59:21: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 06:59:21: #2 alternative fragment length(s) may be 2,46,538 bps INFO @ Fri, 26 Jun 2020 06:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.20_model.r WARNING @ Fri, 26 Jun 2020 06:59:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:59:21: #2 You may need to consider one of the other alternative d(s): 2,46,538 WARNING @ Fri, 26 Jun 2020 06:59:21: #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 06:59:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:59:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:59:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:59:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.10_summits.bed INFO @ Fri, 26 Jun 2020 06:59:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:59:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:59:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:59:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:59:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494934/SRX494934.20_summits.bed INFO @ Fri, 26 Jun 2020 06:59:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 1 millis CompletedMACS2peakCalling