Job ID = 10165804 SRX = SRX8331145 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: 00:03:34 10743677 reads; of these: 10743677 (100.00%) were unpaired; of these: 1610265 (14.99%) aligned 0 times 7229991 (67.30%) aligned exactly 1 time 1903421 (17.72%) aligned >1 times 85.01% overall alignment rate Time searching: 00:03:34 Overall time: 00:03:34 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] 8521464 / 9133412 = 0.9330 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 19:59:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.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 19:59:10: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:59:10: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:59:14: #1 tag size is determined as 61 bps INFO @ Thu, 08 Oct 2020 19:59:14: #1 tag size = 61 INFO @ Thu, 08 Oct 2020 19:59:14: #1 total tags in treatment: 611948 INFO @ Thu, 08 Oct 2020 19:59:14: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:59:14: #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 19:59:14: #1 tags after filtering in treatment: 611948 INFO @ Thu, 08 Oct 2020 19:59:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:59:14: #1 finished! INFO @ Thu, 08 Oct 2020 19:59:14: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:59:14: #2 number of paired peaks: 1771 INFO @ Thu, 08 Oct 2020 19:59:14: start model_add_line... INFO @ Thu, 08 Oct 2020 19:59:14: start X-correlation... INFO @ Thu, 08 Oct 2020 19:59:14: end of X-cor INFO @ Thu, 08 Oct 2020 19:59:14: #2 finished! INFO @ Thu, 08 Oct 2020 19:59:14: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 19:59:14: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 08 Oct 2020 19:59:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.05_model.r WARNING @ Thu, 08 Oct 2020 19:59:14: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:59:14: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 08 Oct 2020 19:59:14: #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 19:59:14: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:59:15: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.05_summits.bed INFO @ Thu, 08 Oct 2020 19:59:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (757 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 19:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.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 19:59:40: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:59:40: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:59:44: #1 tag size is determined as 61 bps INFO @ Thu, 08 Oct 2020 19:59:44: #1 tag size = 61 INFO @ Thu, 08 Oct 2020 19:59:44: #1 total tags in treatment: 611948 INFO @ Thu, 08 Oct 2020 19:59:44: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:59:44: #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 19:59:44: #1 tags after filtering in treatment: 611948 INFO @ Thu, 08 Oct 2020 19:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:59:44: #1 finished! INFO @ Thu, 08 Oct 2020 19:59:44: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:59:44: #2 number of paired peaks: 1771 INFO @ Thu, 08 Oct 2020 19:59:44: start model_add_line... INFO @ Thu, 08 Oct 2020 19:59:44: start X-correlation... INFO @ Thu, 08 Oct 2020 19:59:44: end of X-cor INFO @ Thu, 08 Oct 2020 19:59:44: #2 finished! INFO @ Thu, 08 Oct 2020 19:59:44: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 19:59:44: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 08 Oct 2020 19:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.10_model.r WARNING @ Thu, 08 Oct 2020 19:59:44: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:59:44: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 08 Oct 2020 19:59:44: #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 19:59:44: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:59:45: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:59:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.10_summits.bed INFO @ Thu, 08 Oct 2020 19:59:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (405 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 20:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.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 20:00:10: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:00:10: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:00:14: #1 tag size is determined as 61 bps INFO @ Thu, 08 Oct 2020 20:00:14: #1 tag size = 61 INFO @ Thu, 08 Oct 2020 20:00:14: #1 total tags in treatment: 611948 INFO @ Thu, 08 Oct 2020 20:00:14: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:00:14: #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 20:00:14: #1 tags after filtering in treatment: 611948 INFO @ Thu, 08 Oct 2020 20:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:00:14: #1 finished! INFO @ Thu, 08 Oct 2020 20:00:14: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:00:14: #2 number of paired peaks: 1771 INFO @ Thu, 08 Oct 2020 20:00:14: start model_add_line... INFO @ Thu, 08 Oct 2020 20:00:14: start X-correlation... INFO @ Thu, 08 Oct 2020 20:00:14: end of X-cor INFO @ Thu, 08 Oct 2020 20:00:14: #2 finished! INFO @ Thu, 08 Oct 2020 20:00:14: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 20:00:14: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 08 Oct 2020 20:00:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.20_model.r WARNING @ Thu, 08 Oct 2020 20:00:14: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:00:14: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 08 Oct 2020 20:00:14: #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 20:00:14: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:00:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:00:16: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331145/SRX8331145.20_summits.bed INFO @ Thu, 08 Oct 2020 20:00:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 1 millis CompletedMACS2peakCalling