Job ID = 6368223 SRX = SRX494906 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:58:50 prefetch.2.10.7: 1) Downloading 'SRR1198438'... 2020-06-15T23:58:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:27 prefetch.2.10.7: 1) 'SRR1198438' was downloaded successfully Read 15695316 spots for SRR1198438/SRR1198438.sra Written 15695316 spots for SRR1198438/SRR1198438.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: 00:03:22 15695316 reads; of these: 15695316 (100.00%) were unpaired; of these: 1826656 (11.64%) aligned 0 times 11335177 (72.22%) aligned exactly 1 time 2533483 (16.14%) aligned >1 times 88.36% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 1282341 / 13868660 = 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 09:08:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.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 09:08:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:41: 1000000 INFO @ Tue, 16 Jun 2020 09:08:47: 2000000 INFO @ Tue, 16 Jun 2020 09:08:52: 3000000 INFO @ Tue, 16 Jun 2020 09:08:58: 4000000 INFO @ Tue, 16 Jun 2020 09:09:03: 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 09:09:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.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 09:09:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:09: 6000000 INFO @ Tue, 16 Jun 2020 09:09:11: 1000000 INFO @ Tue, 16 Jun 2020 09:09:15: 7000000 INFO @ Tue, 16 Jun 2020 09:09:17: 2000000 INFO @ Tue, 16 Jun 2020 09:09:21: 8000000 INFO @ Tue, 16 Jun 2020 09:09:23: 3000000 INFO @ Tue, 16 Jun 2020 09:09:27: 9000000 INFO @ Tue, 16 Jun 2020 09:09:29: 4000000 INFO @ Tue, 16 Jun 2020 09:09:33: 10000000 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 09:09:35: 5000000 INFO @ Tue, 16 Jun 2020 09:09:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.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 09:09:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:39: 11000000 INFO @ Tue, 16 Jun 2020 09:09:42: 6000000 INFO @ Tue, 16 Jun 2020 09:09:43: 1000000 INFO @ Tue, 16 Jun 2020 09:09:45: 12000000 INFO @ Tue, 16 Jun 2020 09:09:48: 7000000 INFO @ Tue, 16 Jun 2020 09:09:49: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:09:49: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:09:49: #1 total tags in treatment: 12586319 INFO @ Tue, 16 Jun 2020 09:09:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:49: #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 09:09:49: #1 tags after filtering in treatment: 12586319 INFO @ Tue, 16 Jun 2020 09:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:50: 2000000 INFO @ Tue, 16 Jun 2020 09:09:50: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 09:09:50: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:50: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:09:50: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.05_model.r WARNING @ Tue, 16 Jun 2020 09:09:50: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:50: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:09:50: #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 09:09:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:55: 8000000 INFO @ Tue, 16 Jun 2020 09:09:58: 3000000 INFO @ Tue, 16 Jun 2020 09:10:01: 9000000 INFO @ Tue, 16 Jun 2020 09:10:05: 4000000 INFO @ Tue, 16 Jun 2020 09:10:07: 10000000 INFO @ Tue, 16 Jun 2020 09:10:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:12: 5000000 INFO @ Tue, 16 Jun 2020 09:10:14: 11000000 INFO @ Tue, 16 Jun 2020 09:10:20: 6000000 INFO @ Tue, 16 Jun 2020 09:10:20: 12000000 INFO @ Tue, 16 Jun 2020 09:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.05_summits.bed INFO @ Tue, 16 Jun 2020 09:10:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:10:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:10:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:10:24: #1 total tags in treatment: 12586319 INFO @ Tue, 16 Jun 2020 09:10:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:24: #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 09:10:24: #1 tags after filtering in treatment: 12586319 INFO @ Tue, 16 Jun 2020 09:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:25: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 09:10:25: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:25: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:10:25: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.10_model.r WARNING @ Tue, 16 Jun 2020 09:10:25: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:25: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:10:25: #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 09:10:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:10:26: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:10:33: 8000000 INFO @ Tue, 16 Jun 2020 09:10:39: 9000000 INFO @ Tue, 16 Jun 2020 09:10:45: 10000000 INFO @ Tue, 16 Jun 2020 09:10:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:51: 11000000 INFO @ Tue, 16 Jun 2020 09:10:57: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.10_summits.bed INFO @ Tue, 16 Jun 2020 09:10:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:11:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:11:00: #1 total tags in treatment: 12586319 INFO @ Tue, 16 Jun 2020 09:11:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:00: #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 09:11:00: #1 tags after filtering in treatment: 12586319 INFO @ Tue, 16 Jun 2020 09:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:01: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 09:11:01: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:01: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:11:01: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:01: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:01: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:11:01: #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 09:11:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494906/SRX494906.20_summits.bed INFO @ Tue, 16 Jun 2020 09:11:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling