Job ID = 6368211 SRX = SRX494894 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:09:24 prefetch.2.10.7: 1) Downloading 'SRR1198426'... 2020-06-16T00:09:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:11:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:11:50 prefetch.2.10.7: 1) 'SRR1198426' was downloaded successfully Read 15695316 spots for SRR1198426/SRR1198426.sra Written 15695316 spots for SRR1198426/SRR1198426.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: 00:03:26 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1826689 (11.64%) aligned 0 times 11335213 (72.22%) aligned exactly 1 time 2533414 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1282402 / 13868627 = 0.0925 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 09:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.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 09:20:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:13: 1000000 INFO @ Tue, 16 Jun 2020 09:20:18: 2000000 INFO @ Tue, 16 Jun 2020 09:20:24: 3000000 INFO @ Tue, 16 Jun 2020 09:20:30: 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 @ Tue, 16 Jun 2020 09:20:36: 5000000 INFO @ Tue, 16 Jun 2020 09:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.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 09:20:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:42: 6000000 INFO @ Tue, 16 Jun 2020 09:20:43: 1000000 INFO @ Tue, 16 Jun 2020 09:20:48: 7000000 INFO @ Tue, 16 Jun 2020 09:20:49: 2000000 INFO @ Tue, 16 Jun 2020 09:20:54: 8000000 INFO @ Tue, 16 Jun 2020 09:20:55: 3000000 INFO @ Tue, 16 Jun 2020 09:21:00: 9000000 INFO @ Tue, 16 Jun 2020 09:21:02: 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 09:21:06: 10000000 INFO @ Tue, 16 Jun 2020 09:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.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 09:21:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:08: 5000000 INFO @ Tue, 16 Jun 2020 09:21:13: 11000000 INFO @ Tue, 16 Jun 2020 09:21:14: 1000000 INFO @ Tue, 16 Jun 2020 09:21:14: 6000000 INFO @ Tue, 16 Jun 2020 09:21:19: 12000000 INFO @ Tue, 16 Jun 2020 09:21:20: 2000000 INFO @ Tue, 16 Jun 2020 09:21:21: 7000000 INFO @ Tue, 16 Jun 2020 09:21:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:23: #1 total tags in treatment: 12586225 INFO @ Tue, 16 Jun 2020 09:21:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:23: #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 09:21:23: #1 tags after filtering in treatment: 12586225 INFO @ Tue, 16 Jun 2020 09:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:24: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:21:24: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:24: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:21:24: #2 alternative fragment length(s) may be 2,48,564,577 bps INFO @ Tue, 16 Jun 2020 09:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:24: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:24: #2 You may need to consider one of the other alternative d(s): 2,48,564,577 WARNING @ Tue, 16 Jun 2020 09:21:24: #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 09:21:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:26: 3000000 INFO @ Tue, 16 Jun 2020 09:21:27: 8000000 INFO @ Tue, 16 Jun 2020 09:21:32: 4000000 INFO @ Tue, 16 Jun 2020 09:21:33: 9000000 INFO @ Tue, 16 Jun 2020 09:21:39: 5000000 INFO @ Tue, 16 Jun 2020 09:21:40: 10000000 INFO @ Tue, 16 Jun 2020 09:21:45: 6000000 INFO @ Tue, 16 Jun 2020 09:21:46: 11000000 INFO @ Tue, 16 Jun 2020 09:21:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:51: 7000000 INFO @ Tue, 16 Jun 2020 09:21:52: 12000000 INFO @ Tue, 16 Jun 2020 09:21:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:55: #1 total tags in treatment: 12586225 INFO @ Tue, 16 Jun 2020 09:21:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:55: #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 09:21:56: #1 tags after filtering in treatment: 12586225 INFO @ Tue, 16 Jun 2020 09:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:56: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:21:56: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:57: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:21:57: #2 alternative fragment length(s) may be 2,48,564,577 bps INFO @ Tue, 16 Jun 2020 09:21:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:57: #2 You may need to consider one of the other alternative d(s): 2,48,564,577 WARNING @ Tue, 16 Jun 2020 09:21:57: #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 09:21:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:57: 8000000 INFO @ Tue, 16 Jun 2020 09:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.05_summits.bed INFO @ Tue, 16 Jun 2020 09:22:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (649 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:03: 9000000 INFO @ Tue, 16 Jun 2020 09:22:09: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:22:14: 11000000 INFO @ Tue, 16 Jun 2020 09:22:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:20: 12000000 INFO @ Tue, 16 Jun 2020 09:22:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:24: #1 total tags in treatment: 12586225 INFO @ Tue, 16 Jun 2020 09:22:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:24: #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 09:22:24: #1 tags after filtering in treatment: 12586225 INFO @ Tue, 16 Jun 2020 09:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:25: #2 number of paired peaks: 349 WARNING @ Tue, 16 Jun 2020 09:22:25: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:25: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:22:25: #2 alternative fragment length(s) may be 2,48,564,577 bps INFO @ Tue, 16 Jun 2020 09:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.20_model.r WARNING @ Tue, 16 Jun 2020 09:22:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:25: #2 You may need to consider one of the other alternative d(s): 2,48,564,577 WARNING @ Tue, 16 Jun 2020 09:22:25: #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 09:22:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (501 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:22:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494894/SRX494894.20_summits.bed INFO @ Tue, 16 Jun 2020 09:23:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling