Job ID = 14168077 SRX = SRX8688954 Genome = dm6 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: 00:01:50 6874534 reads; of these: 6874534 (100.00%) were unpaired; of these: 511990 (7.45%) aligned 0 times 5217891 (75.90%) aligned exactly 1 time 1144653 (16.65%) aligned >1 times 92.55% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 385329 / 6362544 = 0.0606 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 @ Fri, 10 Dec 2021 15:09:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 15:09:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:09:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:10:04: 1000000 INFO @ Fri, 10 Dec 2021 15:10:11: 2000000 INFO @ Fri, 10 Dec 2021 15:10:18: 3000000 INFO @ Fri, 10 Dec 2021 15:10:24: 4000000 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 @ Fri, 10 Dec 2021 15:10:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 15:10:26: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:10:26: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:10:32: 5000000 INFO @ Fri, 10 Dec 2021 15:10:34: 1000000 INFO @ Fri, 10 Dec 2021 15:10:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:10:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:10:39: #1 total tags in treatment: 5977215 INFO @ Fri, 10 Dec 2021 15:10:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:10:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:10:40: #1 tags after filtering in treatment: 5977181 INFO @ Fri, 10 Dec 2021 15:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:10:40: #1 finished! INFO @ Fri, 10 Dec 2021 15:10:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:10:40: #2 number of paired peaks: 132 WARNING @ Fri, 10 Dec 2021 15:10:40: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Dec 2021 15:10:40: start model_add_line... INFO @ Fri, 10 Dec 2021 15:10:40: start X-correlation... INFO @ Fri, 10 Dec 2021 15:10:40: end of X-cor INFO @ Fri, 10 Dec 2021 15:10:40: #2 finished! INFO @ Fri, 10 Dec 2021 15:10:40: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 15:10:40: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Dec 2021 15:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.05_model.r WARNING @ Fri, 10 Dec 2021 15:10:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:10:40: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Dec 2021 15:10:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:10:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:10:42: 2000000 INFO @ Fri, 10 Dec 2021 15:10:49: 3000000 INFO @ Fri, 10 Dec 2021 15:10:53: #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 @ Fri, 10 Dec 2021 15:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Fri, 10 Dec 2021 15:10:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:10:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:10:56: 4000000 INFO @ Fri, 10 Dec 2021 15:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.05_summits.bed INFO @ Fri, 10 Dec 2021 15:11:00: Done! pass1 - making usageList (132 chroms): 0 millis pass2 - checking and writing primary data (319 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:11:04: 1000000 INFO @ Fri, 10 Dec 2021 15:11:04: 5000000 INFO @ Fri, 10 Dec 2021 15:11:11: 2000000 INFO @ Fri, 10 Dec 2021 15:11:13: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:11:13: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:11:13: #1 total tags in treatment: 5977215 INFO @ Fri, 10 Dec 2021 15:11:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:11:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:11:13: #1 tags after filtering in treatment: 5977181 INFO @ Fri, 10 Dec 2021 15:11:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:11:13: #1 finished! INFO @ Fri, 10 Dec 2021 15:11:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:11:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:11:13: #2 number of paired peaks: 132 WARNING @ Fri, 10 Dec 2021 15:11:13: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Dec 2021 15:11:13: start model_add_line... INFO @ Fri, 10 Dec 2021 15:11:13: start X-correlation... INFO @ Fri, 10 Dec 2021 15:11:13: end of X-cor INFO @ Fri, 10 Dec 2021 15:11:13: #2 finished! INFO @ Fri, 10 Dec 2021 15:11:13: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 15:11:13: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Dec 2021 15:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.10_model.r WARNING @ Fri, 10 Dec 2021 15:11:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:11:13: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Dec 2021 15:11:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:11:13: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:11:18: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:11:24: 4000000 INFO @ Fri, 10 Dec 2021 15:11:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:11:30: 5000000 INFO @ Fri, 10 Dec 2021 15:11:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.10_summits.bed INFO @ Fri, 10 Dec 2021 15:11:32: Done! pass1 - making usageList (91 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:11:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:11:37: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:11:37: #1 total tags in treatment: 5977215 INFO @ Fri, 10 Dec 2021 15:11:37: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:11:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:11:37: #1 tags after filtering in treatment: 5977181 INFO @ Fri, 10 Dec 2021 15:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:11:37: #1 finished! INFO @ Fri, 10 Dec 2021 15:11:37: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:11:37: #2 number of paired peaks: 132 WARNING @ Fri, 10 Dec 2021 15:11:37: Fewer paired peaks (132) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 132 pairs to build model! INFO @ Fri, 10 Dec 2021 15:11:37: start model_add_line... INFO @ Fri, 10 Dec 2021 15:11:38: start X-correlation... INFO @ Fri, 10 Dec 2021 15:11:38: end of X-cor INFO @ Fri, 10 Dec 2021 15:11:38: #2 finished! INFO @ Fri, 10 Dec 2021 15:11:38: #2 predicted fragment length is 53 bps INFO @ Fri, 10 Dec 2021 15:11:38: #2 alternative fragment length(s) may be 53 bps INFO @ Fri, 10 Dec 2021 15:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.20_model.r WARNING @ Fri, 10 Dec 2021 15:11:38: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:11:38: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Fri, 10 Dec 2021 15:11:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:11:38: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:11:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688954/SRX8688954.20_summits.bed INFO @ Fri, 10 Dec 2021 15:11:56: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (99 records, 4 fields): 4 millis CompletedMACS2peakCalling