Job ID = 14160610 SRX = SRX9904334 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: 00:01:35 5635197 reads; of these: 5635197 (100.00%) were unpaired; of these: 1790486 (31.77%) aligned 0 times 2790131 (49.51%) aligned exactly 1 time 1054580 (18.71%) aligned >1 times 68.23% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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] 404239 / 3844711 = 0.1051 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 @ Thu, 09 Dec 2021 03:28:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.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, 09 Dec 2021 03:28:16: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:28:16: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:25: 1000000 INFO @ Thu, 09 Dec 2021 03:28:33: 2000000 INFO @ Thu, 09 Dec 2021 03:28:41: 3000000 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 @ Thu, 09 Dec 2021 03:28:45: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:28:45: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:28:45: #1 total tags in treatment: 3440472 INFO @ Thu, 09 Dec 2021 03:28:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:28:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:28:45: #1 tags after filtering in treatment: 3440472 INFO @ Thu, 09 Dec 2021 03:28:45: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:28:45: #1 finished! INFO @ Thu, 09 Dec 2021 03:28:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:28:45: #2 number of paired peaks: 1177 INFO @ Thu, 09 Dec 2021 03:28:45: start model_add_line... INFO @ Thu, 09 Dec 2021 03:28:45: start X-correlation... INFO @ Thu, 09 Dec 2021 03:28:45: end of X-cor INFO @ Thu, 09 Dec 2021 03:28:45: #2 finished! INFO @ Thu, 09 Dec 2021 03:28:45: #2 predicted fragment length is 54 bps INFO @ Thu, 09 Dec 2021 03:28:45: #2 alternative fragment length(s) may be 4,54 bps INFO @ Thu, 09 Dec 2021 03:28:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.05_model.r WARNING @ Thu, 09 Dec 2021 03:28:45: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:28:45: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Thu, 09 Dec 2021 03:28:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:28:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:28:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:28:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.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, 09 Dec 2021 03:28:46: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:28:46: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:28:55: 1000000 INFO @ Thu, 09 Dec 2021 03:28:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.05_summits.bed INFO @ Thu, 09 Dec 2021 03:29:03: Done! INFO @ Thu, 09 Dec 2021 03:29:03: 2000000 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (596 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:11: 3000000 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 @ Thu, 09 Dec 2021 03:29:15: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:29:15: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:29:15: #1 total tags in treatment: 3440472 INFO @ Thu, 09 Dec 2021 03:29:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:29:15: #1 tags after filtering in treatment: 3440472 INFO @ Thu, 09 Dec 2021 03:29:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:29:15: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:15: #2 number of paired peaks: 1177 INFO @ Thu, 09 Dec 2021 03:29:15: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:15: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:15: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:15: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:15: #2 predicted fragment length is 54 bps INFO @ Thu, 09 Dec 2021 03:29:15: #2 alternative fragment length(s) may be 4,54 bps INFO @ Thu, 09 Dec 2021 03:29:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.10_model.r WARNING @ Thu, 09 Dec 2021 03:29:15: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:29:15: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Thu, 09 Dec 2021 03:29:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:29:15: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:29:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.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, 09 Dec 2021 03:29:16: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:29:16: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:29:26: 1000000 INFO @ Thu, 09 Dec 2021 03:29:27: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:29:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.10_summits.bed INFO @ Thu, 09 Dec 2021 03:29:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:29:35: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:29:44: 3000000 INFO @ Thu, 09 Dec 2021 03:29:48: #1 tag size is determined as 50 bps INFO @ Thu, 09 Dec 2021 03:29:48: #1 tag size = 50 INFO @ Thu, 09 Dec 2021 03:29:48: #1 total tags in treatment: 3440472 INFO @ Thu, 09 Dec 2021 03:29:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:29:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:29:48: #1 tags after filtering in treatment: 3440472 INFO @ Thu, 09 Dec 2021 03:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:29:48: #1 finished! INFO @ Thu, 09 Dec 2021 03:29:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:29:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:29:48: #2 number of paired peaks: 1177 INFO @ Thu, 09 Dec 2021 03:29:48: start model_add_line... INFO @ Thu, 09 Dec 2021 03:29:48: start X-correlation... INFO @ Thu, 09 Dec 2021 03:29:48: end of X-cor INFO @ Thu, 09 Dec 2021 03:29:48: #2 finished! INFO @ Thu, 09 Dec 2021 03:29:48: #2 predicted fragment length is 54 bps INFO @ Thu, 09 Dec 2021 03:29:48: #2 alternative fragment length(s) may be 4,54 bps INFO @ Thu, 09 Dec 2021 03:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.20_model.r WARNING @ Thu, 09 Dec 2021 03:29:48: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:29:48: #2 You may need to consider one of the other alternative d(s): 4,54 WARNING @ Thu, 09 Dec 2021 03:29:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:29:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:29:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:30:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9904334/SRX9904334.20_summits.bed INFO @ Thu, 09 Dec 2021 03:30:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling