Job ID = 14158116 SRX = SRX6717205 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: 00:02:42 16001701 reads; of these: 16001701 (100.00%) were unpaired; of these: 13453308 (84.07%) aligned 0 times 2296468 (14.35%) aligned exactly 1 time 251925 (1.57%) aligned >1 times 15.93% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 838227 / 2548393 = 0.3289 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:32:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.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 @ Wed, 08 Dec 2021 14:32:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:28: 1000000 INFO @ Wed, 08 Dec 2021 14:32:33: #1 tag size is determined as 76 bps INFO @ Wed, 08 Dec 2021 14:32:33: #1 tag size = 76 INFO @ Wed, 08 Dec 2021 14:32:33: #1 total tags in treatment: 1710166 INFO @ Wed, 08 Dec 2021 14:32:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:32:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:32:33: #1 tags after filtering in treatment: 1710166 INFO @ Wed, 08 Dec 2021 14:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:32:33: #1 finished! INFO @ Wed, 08 Dec 2021 14:32:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:32:34: #2 number of paired peaks: 3306 INFO @ Wed, 08 Dec 2021 14:32:34: start model_add_line... INFO @ Wed, 08 Dec 2021 14:32:34: start X-correlation... INFO @ Wed, 08 Dec 2021 14:32:34: end of X-cor INFO @ Wed, 08 Dec 2021 14:32:34: #2 finished! INFO @ Wed, 08 Dec 2021 14:32:34: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 14:32:34: #2 alternative fragment length(s) may be 144 bps INFO @ Wed, 08 Dec 2021 14:32:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.05_model.r WARNING @ Wed, 08 Dec 2021 14:32:34: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:32:34: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Wed, 08 Dec 2021 14:32:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:32:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:32:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:32:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.05_summits.bed INFO @ Wed, 08 Dec 2021 14:32:40: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7773 records, 4 fields): 8 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:32:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.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 @ Wed, 08 Dec 2021 14:32:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:58: 1000000 INFO @ Wed, 08 Dec 2021 14:33:03: #1 tag size is determined as 76 bps INFO @ Wed, 08 Dec 2021 14:33:03: #1 tag size = 76 INFO @ Wed, 08 Dec 2021 14:33:03: #1 total tags in treatment: 1710166 INFO @ Wed, 08 Dec 2021 14:33:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:33:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:33:03: #1 tags after filtering in treatment: 1710166 INFO @ Wed, 08 Dec 2021 14:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:33:03: #1 finished! INFO @ Wed, 08 Dec 2021 14:33:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:33:03: #2 number of paired peaks: 3306 INFO @ Wed, 08 Dec 2021 14:33:03: start model_add_line... INFO @ Wed, 08 Dec 2021 14:33:03: start X-correlation... INFO @ Wed, 08 Dec 2021 14:33:03: end of X-cor INFO @ Wed, 08 Dec 2021 14:33:03: #2 finished! INFO @ Wed, 08 Dec 2021 14:33:03: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 14:33:03: #2 alternative fragment length(s) may be 144 bps INFO @ Wed, 08 Dec 2021 14:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.10_model.r WARNING @ Wed, 08 Dec 2021 14:33:03: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:33:03: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Wed, 08 Dec 2021 14:33:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:33:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:33:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:33:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:33:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:33:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:33:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.10_summits.bed INFO @ Wed, 08 Dec 2021 14:33:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4458 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:33:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.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 @ Wed, 08 Dec 2021 14:33:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:33:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:33:27: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:33:32: #1 tag size is determined as 76 bps INFO @ Wed, 08 Dec 2021 14:33:32: #1 tag size = 76 INFO @ Wed, 08 Dec 2021 14:33:32: #1 total tags in treatment: 1710166 INFO @ Wed, 08 Dec 2021 14:33:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:33:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:33:32: #1 tags after filtering in treatment: 1710166 INFO @ Wed, 08 Dec 2021 14:33:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:33:32: #1 finished! INFO @ Wed, 08 Dec 2021 14:33:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:33:32: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:33:32: #2 number of paired peaks: 3306 INFO @ Wed, 08 Dec 2021 14:33:32: start model_add_line... INFO @ Wed, 08 Dec 2021 14:33:32: start X-correlation... INFO @ Wed, 08 Dec 2021 14:33:32: end of X-cor INFO @ Wed, 08 Dec 2021 14:33:32: #2 finished! INFO @ Wed, 08 Dec 2021 14:33:32: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 14:33:32: #2 alternative fragment length(s) may be 144 bps INFO @ Wed, 08 Dec 2021 14:33:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.20_model.r WARNING @ Wed, 08 Dec 2021 14:33:32: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:33:32: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Wed, 08 Dec 2021 14:33:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:33:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:33:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:33:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:33:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:33:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:33:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6717205/SRX6717205.20_summits.bed INFO @ Wed, 08 Dec 2021 14:33:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2235 records, 4 fields): 3 millis CompletedMACS2peakCalling