Job ID = 10165822 SRX = SRX8832071 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:02:14 15379429 reads; of these: 15379429 (100.00%) were unpaired; of these: 9408898 (61.18%) aligned 0 times 4046601 (26.31%) aligned exactly 1 time 1923930 (12.51%) aligned >1 times 38.82% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 1639309 / 5970531 = 0.2746 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 @ Thu, 08 Oct 2020 20:00:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.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 @ Thu, 08 Oct 2020 20:00:29: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:00:29: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:00:34: 1000000 INFO @ Thu, 08 Oct 2020 20:00:38: 2000000 INFO @ Thu, 08 Oct 2020 20:00:43: 3000000 INFO @ Thu, 08 Oct 2020 20:00:48: 4000000 INFO @ Thu, 08 Oct 2020 20:00:49: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:00:49: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:00:49: #1 total tags in treatment: 4331222 INFO @ Thu, 08 Oct 2020 20:00:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:00:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:00:49: #1 tags after filtering in treatment: 4331222 INFO @ Thu, 08 Oct 2020 20:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:00:49: #1 finished! INFO @ Thu, 08 Oct 2020 20:00:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:00:50: #2 number of paired peaks: 2135 INFO @ Thu, 08 Oct 2020 20:00:50: start model_add_line... INFO @ Thu, 08 Oct 2020 20:00:50: start X-correlation... INFO @ Thu, 08 Oct 2020 20:00:50: end of X-cor INFO @ Thu, 08 Oct 2020 20:00:50: #2 finished! INFO @ Thu, 08 Oct 2020 20:00:50: #2 predicted fragment length is 100 bps INFO @ Thu, 08 Oct 2020 20:00:50: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 08 Oct 2020 20:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.05_model.r WARNING @ Thu, 08 Oct 2020 20:00:50: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:00:50: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 08 Oct 2020 20:00:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:00:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:00:50: #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 @ Thu, 08 Oct 2020 20:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.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 @ Thu, 08 Oct 2020 20:00:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:00:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:01:00: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:01:04: 1000000 INFO @ Thu, 08 Oct 2020 20:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.05_summits.bed INFO @ Thu, 08 Oct 2020 20:01:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3879 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:01:10: 2000000 INFO @ Thu, 08 Oct 2020 20:01:15: 3000000 INFO @ Thu, 08 Oct 2020 20:01:20: 4000000 INFO @ Thu, 08 Oct 2020 20:01:22: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:01:22: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:01:22: #1 total tags in treatment: 4331222 INFO @ Thu, 08 Oct 2020 20:01:22: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:01:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:01:22: #1 tags after filtering in treatment: 4331222 INFO @ Thu, 08 Oct 2020 20:01:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:01:22: #1 finished! INFO @ Thu, 08 Oct 2020 20:01:22: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:01:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:01:23: #2 number of paired peaks: 2135 INFO @ Thu, 08 Oct 2020 20:01:23: start model_add_line... INFO @ Thu, 08 Oct 2020 20:01:23: start X-correlation... INFO @ Thu, 08 Oct 2020 20:01:23: end of X-cor INFO @ Thu, 08 Oct 2020 20:01:23: #2 finished! INFO @ Thu, 08 Oct 2020 20:01:23: #2 predicted fragment length is 100 bps INFO @ Thu, 08 Oct 2020 20:01:23: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 08 Oct 2020 20:01:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.10_model.r WARNING @ Thu, 08 Oct 2020 20:01:23: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:01:23: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 08 Oct 2020 20:01:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:01:23: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:01:23: #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 @ Thu, 08 Oct 2020 20:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.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 @ Thu, 08 Oct 2020 20:01:30: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:01:30: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:01:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:01:35: 1000000 INFO @ Thu, 08 Oct 2020 20:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.10_summits.bed INFO @ Thu, 08 Oct 2020 20:01:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1762 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:01:40: 2000000 INFO @ Thu, 08 Oct 2020 20:01:44: 3000000 INFO @ Thu, 08 Oct 2020 20:01:49: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:01:51: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:01:51: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:01:51: #1 total tags in treatment: 4331222 INFO @ Thu, 08 Oct 2020 20:01:51: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:01:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:01:51: #1 tags after filtering in treatment: 4331222 INFO @ Thu, 08 Oct 2020 20:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:01:51: #1 finished! INFO @ Thu, 08 Oct 2020 20:01:51: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:01:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:01:51: #2 number of paired peaks: 2135 INFO @ Thu, 08 Oct 2020 20:01:51: start model_add_line... INFO @ Thu, 08 Oct 2020 20:01:51: start X-correlation... INFO @ Thu, 08 Oct 2020 20:01:51: end of X-cor INFO @ Thu, 08 Oct 2020 20:01:51: #2 finished! INFO @ Thu, 08 Oct 2020 20:01:51: #2 predicted fragment length is 100 bps INFO @ Thu, 08 Oct 2020 20:01:51: #2 alternative fragment length(s) may be 100 bps INFO @ Thu, 08 Oct 2020 20:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.20_model.r WARNING @ Thu, 08 Oct 2020 20:01:51: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:01:51: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Thu, 08 Oct 2020 20:01:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:01:51: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:01:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:02:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8832071/SRX8832071.20_summits.bed INFO @ Thu, 08 Oct 2020 20:02:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 millis CompletedMACS2peakCalling