Job ID = 6368719 SRX = SRX5402743 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:51 prefetch.2.10.7: 1) Downloading 'SRR8602977'... 2020-06-16T00:22:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:24 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:24 prefetch.2.10.7: 1) 'SRR8602977' was downloaded successfully Read 23575875 spots for SRR8602977/SRR8602977.sra Written 23575875 spots for SRR8602977/SRR8602977.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: 00:03:35 23575875 reads; of these: 23575875 (100.00%) were unpaired; of these: 15517847 (65.82%) aligned 0 times 4961708 (21.05%) aligned exactly 1 time 3096320 (13.13%) aligned >1 times 34.18% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_rmdupse_core] 1669390 / 8058028 = 0.2072 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 09:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.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 09:32:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:27: 1000000 INFO @ Tue, 16 Jun 2020 09:32:33: 2000000 INFO @ Tue, 16 Jun 2020 09:32:39: 3000000 INFO @ Tue, 16 Jun 2020 09:32:45: 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 09:32:51: 5000000 INFO @ Tue, 16 Jun 2020 09:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.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 09:32:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:57: 6000000 INFO @ Tue, 16 Jun 2020 09:32:58: 1000000 INFO @ Tue, 16 Jun 2020 09:32:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:32:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:32:59: #1 total tags in treatment: 6388638 INFO @ Tue, 16 Jun 2020 09:32:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:59: #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 09:32:59: #1 tags after filtering in treatment: 6388638 INFO @ Tue, 16 Jun 2020 09:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:00: #2 number of paired peaks: 1704 INFO @ Tue, 16 Jun 2020 09:33:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:00: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:33:00: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 16 Jun 2020 09:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:00: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 16 Jun 2020 09:33:00: #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 09:33:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:04: 2000000 INFO @ Tue, 16 Jun 2020 09:33:09: 3000000 INFO @ Tue, 16 Jun 2020 09:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:15: 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 09:33:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2725 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:21: 5000000 INFO @ Tue, 16 Jun 2020 09:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.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 09:33:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:27: 6000000 INFO @ Tue, 16 Jun 2020 09:33:27: 1000000 INFO @ Tue, 16 Jun 2020 09:33:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:33:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:33:29: #1 total tags in treatment: 6388638 INFO @ Tue, 16 Jun 2020 09:33:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:29: #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 09:33:29: #1 tags after filtering in treatment: 6388638 INFO @ Tue, 16 Jun 2020 09:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:30: #2 number of paired peaks: 1704 INFO @ Tue, 16 Jun 2020 09:33:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:30: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:33:30: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 16 Jun 2020 09:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:30: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:30: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 16 Jun 2020 09:33:30: #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 09:33:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:33: 2000000 INFO @ Tue, 16 Jun 2020 09:33:39: 3000000 INFO @ Tue, 16 Jun 2020 09:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:45: 4000000 INFO @ Tue, 16 Jun 2020 09:33:50: 5000000 INFO @ Tue, 16 Jun 2020 09:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1100 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:56: 6000000 INFO @ Tue, 16 Jun 2020 09:33:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:33:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:33:58: #1 total tags in treatment: 6388638 INFO @ Tue, 16 Jun 2020 09:33:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:58: #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 09:33:58: #1 tags after filtering in treatment: 6388638 INFO @ Tue, 16 Jun 2020 09:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:59: #2 number of paired peaks: 1704 INFO @ Tue, 16 Jun 2020 09:33:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:59: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:33:59: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 16 Jun 2020 09:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:59: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 16 Jun 2020 09:33:59: #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 09:33:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402743/SRX5402743.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling