Job ID = 6368186 SRX = SRX494870 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:14:47 prefetch.2.10.7: 1) Downloading 'SRR1198402'... 2020-06-16T00:14:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:17:40 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:17:40 prefetch.2.10.7: 1) 'SRR1198402' was downloaded successfully Read 29910991 spots for SRR1198402/SRR1198402.sra Written 29910991 spots for SRR1198402/SRR1198402.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: 00:06:45 29910991 reads; of these: 29910991 (100.00%) were unpaired; of these: 1155519 (3.86%) aligned 0 times 24595047 (82.23%) aligned exactly 1 time 4160425 (13.91%) aligned >1 times 96.14% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 24777900 / 28755472 = 0.8617 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 09:30:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.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 09:30:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:52: 1000000 INFO @ Tue, 16 Jun 2020 09:30:58: 2000000 INFO @ Tue, 16 Jun 2020 09:31:04: 3000000 INFO @ Tue, 16 Jun 2020 09:31:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:10: #1 total tags in treatment: 3977572 INFO @ Tue, 16 Jun 2020 09:31:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:10: #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 09:31:10: #1 tags after filtering in treatment: 3977572 INFO @ Tue, 16 Jun 2020 09:31:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:10: #2 number of paired peaks: 1121 INFO @ Tue, 16 Jun 2020 09:31:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:10: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:31:10: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 09:31:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:10: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:10: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 09:31:10: #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 09:31:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:10: #3 Pre-compute pvalue-qvalue table... 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 09:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.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 09:31:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:22: 1000000 INFO @ Tue, 16 Jun 2020 09:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1560 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:28: 2000000 INFO @ Tue, 16 Jun 2020 09:31:35: 3000000 INFO @ Tue, 16 Jun 2020 09:31:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:31:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:31:41: #1 total tags in treatment: 3977572 INFO @ Tue, 16 Jun 2020 09:31:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:41: #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 09:31:41: #1 tags after filtering in treatment: 3977572 INFO @ Tue, 16 Jun 2020 09:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:41: #2 number of paired peaks: 1121 INFO @ Tue, 16 Jun 2020 09:31:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:41: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:31:41: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 09:31:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.10_model.r WARNING @ Tue, 16 Jun 2020 09:31:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:41: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 09:31:41: #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 09:31:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:41: #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 09:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.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 09:31:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:52: 1000000 INFO @ Tue, 16 Jun 2020 09:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (866 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:58: 2000000 INFO @ Tue, 16 Jun 2020 09:32:04: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:32:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:32:10: #1 total tags in treatment: 3977572 INFO @ Tue, 16 Jun 2020 09:32:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:10: #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 09:32:10: #1 tags after filtering in treatment: 3977572 INFO @ Tue, 16 Jun 2020 09:32:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:11: #2 number of paired peaks: 1121 INFO @ Tue, 16 Jun 2020 09:32:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:11: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:32:11: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 09:32:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:11: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 09:32:11: #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 09:32:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494870/SRX494870.20_summits.bed INFO @ Tue, 16 Jun 2020 09:32:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (351 records, 4 fields): 2 millis CompletedMACS2peakCalling