Job ID = 14158795 SRX = SRX7665443 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: 00:02:06 14610558 reads; of these: 14610558 (100.00%) were unpaired; of these: 8972241 (61.41%) aligned 0 times 4732341 (32.39%) aligned exactly 1 time 905976 (6.20%) aligned >1 times 38.59% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 1012443 / 5638317 = 0.1796 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 18:00:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.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 18:00:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:00:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:00:26: 1000000 INFO @ Wed, 08 Dec 2021 18:00:35: 2000000 INFO @ Wed, 08 Dec 2021 18:00:43: 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 @ Wed, 08 Dec 2021 18:00:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.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 18:00:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:00:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:00:51: 4000000 INFO @ Wed, 08 Dec 2021 18:00:57: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 18:00:57: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 18:00:57: #1 total tags in treatment: 4625874 INFO @ Wed, 08 Dec 2021 18:00:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:00:57: #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 18:00:57: #1 tags after filtering in treatment: 4625874 INFO @ Wed, 08 Dec 2021 18:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:00:57: #1 finished! INFO @ Wed, 08 Dec 2021 18:00:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:00:57: #2 number of paired peaks: 564 WARNING @ Wed, 08 Dec 2021 18:00:57: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Wed, 08 Dec 2021 18:00:57: start model_add_line... INFO @ Wed, 08 Dec 2021 18:00:57: start X-correlation... INFO @ Wed, 08 Dec 2021 18:00:57: end of X-cor INFO @ Wed, 08 Dec 2021 18:00:57: #2 finished! INFO @ Wed, 08 Dec 2021 18:00:57: #2 predicted fragment length is 88 bps INFO @ Wed, 08 Dec 2021 18:00:57: #2 alternative fragment length(s) may be 88 bps INFO @ Wed, 08 Dec 2021 18:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.05_model.r WARNING @ Wed, 08 Dec 2021 18:00:57: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:00:57: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Wed, 08 Dec 2021 18:00:57: #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 18:00:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:00:58: 1000000 INFO @ Wed, 08 Dec 2021 18:01:08: 2000000 INFO @ Wed, 08 Dec 2021 18:01:11: #3 Call peaks for each chromosome... 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 18:01:17: 3000000 INFO @ Wed, 08 Dec 2021 18:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.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 18:01:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:01:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.05_summits.bed INFO @ Wed, 08 Dec 2021 18:01:18: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1859 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:01:27: 1000000 INFO @ Wed, 08 Dec 2021 18:01:27: 4000000 INFO @ Wed, 08 Dec 2021 18:01:33: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 18:01:33: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 18:01:33: #1 total tags in treatment: 4625874 INFO @ Wed, 08 Dec 2021 18:01:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:01:33: #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 18:01:34: #1 tags after filtering in treatment: 4625874 INFO @ Wed, 08 Dec 2021 18:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:01:34: #1 finished! INFO @ Wed, 08 Dec 2021 18:01:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:01:34: #2 number of paired peaks: 564 WARNING @ Wed, 08 Dec 2021 18:01:34: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Wed, 08 Dec 2021 18:01:34: start model_add_line... INFO @ Wed, 08 Dec 2021 18:01:34: start X-correlation... INFO @ Wed, 08 Dec 2021 18:01:34: end of X-cor INFO @ Wed, 08 Dec 2021 18:01:34: #2 finished! INFO @ Wed, 08 Dec 2021 18:01:34: #2 predicted fragment length is 88 bps INFO @ Wed, 08 Dec 2021 18:01:34: #2 alternative fragment length(s) may be 88 bps INFO @ Wed, 08 Dec 2021 18:01:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.10_model.r WARNING @ Wed, 08 Dec 2021 18:01:34: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:01:34: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Wed, 08 Dec 2021 18:01:34: #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 18:01:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:01:35: 2000000 INFO @ Wed, 08 Dec 2021 18:01:43: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:01:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:01:51: 4000000 INFO @ Wed, 08 Dec 2021 18:01:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:01:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:01:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.10_summits.bed INFO @ Wed, 08 Dec 2021 18:01:56: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1036 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:01:56: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 18:01:56: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 18:01:56: #1 total tags in treatment: 4625874 INFO @ Wed, 08 Dec 2021 18:01:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:01:56: #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 18:01:57: #1 tags after filtering in treatment: 4625874 INFO @ Wed, 08 Dec 2021 18:01:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:01:57: #1 finished! INFO @ Wed, 08 Dec 2021 18:01:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:01:57: #2 number of paired peaks: 564 WARNING @ Wed, 08 Dec 2021 18:01:57: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Wed, 08 Dec 2021 18:01:57: start model_add_line... INFO @ Wed, 08 Dec 2021 18:01:57: start X-correlation... INFO @ Wed, 08 Dec 2021 18:01:57: end of X-cor INFO @ Wed, 08 Dec 2021 18:01:57: #2 finished! INFO @ Wed, 08 Dec 2021 18:01:57: #2 predicted fragment length is 88 bps INFO @ Wed, 08 Dec 2021 18:01:57: #2 alternative fragment length(s) may be 88 bps INFO @ Wed, 08 Dec 2021 18:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.20_model.r WARNING @ Wed, 08 Dec 2021 18:01:57: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:01:57: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Wed, 08 Dec 2021 18:01:57: #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 18:01:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:01:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:02:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665443/SRX7665443.20_summits.bed INFO @ Wed, 08 Dec 2021 18:02:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling