Job ID = 14170941 SRX = SRX8689086 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: 00:00:01 Multiseed full-index search: 00:02:17 6506928 reads; of these: 6506928 (100.00%) were unpaired; of these: 194731 (2.99%) aligned 0 times 4494974 (69.08%) aligned exactly 1 time 1817223 (27.93%) aligned >1 times 97.01% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 401592 / 6312197 = 0.0636 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 @ Sat, 11 Dec 2021 09:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.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 @ Sat, 11 Dec 2021 09:06:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:50: 1000000 INFO @ Sat, 11 Dec 2021 09:07:00: 2000000 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 @ Sat, 11 Dec 2021 09:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.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 @ Sat, 11 Dec 2021 09:07:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:11: 3000000 INFO @ Sat, 11 Dec 2021 09:07:21: 1000000 INFO @ Sat, 11 Dec 2021 09:07:22: 4000000 INFO @ Sat, 11 Dec 2021 09:07:33: 2000000 INFO @ Sat, 11 Dec 2021 09:07:34: 5000000 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 @ Sat, 11 Dec 2021 09:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.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 @ Sat, 11 Dec 2021 09:07:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:44: #1 total tags in treatment: 5910605 INFO @ Sat, 11 Dec 2021 09:07:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:07:45: 3000000 INFO @ Sat, 11 Dec 2021 09:07:45: #1 tags after filtering in treatment: 5910423 INFO @ Sat, 11 Dec 2021 09:07:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:45: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:46: #2 number of paired peaks: 1045 INFO @ Sat, 11 Dec 2021 09:07:46: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:46: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:46: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:46: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:46: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 09:07:46: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 11 Dec 2021 09:07:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.05_model.r WARNING @ Sat, 11 Dec 2021 09:07:46: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:46: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 11 Dec 2021 09:07:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:07:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:51: 1000000 INFO @ Sat, 11 Dec 2021 09:07:55: 4000000 INFO @ Sat, 11 Dec 2021 09:08:02: 2000000 INFO @ Sat, 11 Dec 2021 09:08:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:07: 5000000 INFO @ Sat, 11 Dec 2021 09:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.05_summits.bed INFO @ Sat, 11 Dec 2021 09:08:12: Done! pass1 - making usageList (588 chroms): 3 millis pass2 - checking and writing primary data (2206 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:13: 3000000 INFO @ Sat, 11 Dec 2021 09:08:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:08:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:08:16: #1 total tags in treatment: 5910605 INFO @ Sat, 11 Dec 2021 09:08:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:08:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:08:17: #1 tags after filtering in treatment: 5910423 INFO @ Sat, 11 Dec 2021 09:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:17: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:17: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:08:17: #2 number of paired peaks: 1045 INFO @ Sat, 11 Dec 2021 09:08:17: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:17: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:18: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:18: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:18: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 09:08:18: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 11 Dec 2021 09:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.10_model.r WARNING @ Sat, 11 Dec 2021 09:08:18: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:18: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 11 Dec 2021 09:08:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:08:18: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:08:24: 4000000 INFO @ Sat, 11 Dec 2021 09:08:35: 5000000 INFO @ Sat, 11 Dec 2021 09:08:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.10_summits.bed INFO @ Sat, 11 Dec 2021 09:08:44: Done! pass1 - making usageList (420 chroms): 2 millis INFO @ Sat, 11 Dec 2021 09:08:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:08:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:08:44: #1 total tags in treatment: 5910605 INFO @ Sat, 11 Dec 2021 09:08:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:08:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (1061 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:45: #1 tags after filtering in treatment: 5910423 INFO @ Sat, 11 Dec 2021 09:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:45: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:45: #2 number of paired peaks: 1045 INFO @ Sat, 11 Dec 2021 09:08:45: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:45: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:45: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:45: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:45: #2 predicted fragment length is 56 bps INFO @ Sat, 11 Dec 2021 09:08:45: #2 alternative fragment length(s) may be 56 bps INFO @ Sat, 11 Dec 2021 09:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.20_model.r WARNING @ Sat, 11 Dec 2021 09:08:45: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:45: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sat, 11 Dec 2021 09:08:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:08:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:09:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:09:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:09:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689086/SRX8689086.20_summits.bed INFO @ Sat, 11 Dec 2021 09:09:12: Done! pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (315 records, 4 fields): 15 millis CompletedMACS2peakCalling