Job ID = 14170940 SRX = SRX8689084 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: 00:02:44 8383850 reads; of these: 8383850 (100.00%) were unpaired; of these: 409977 (4.89%) aligned 0 times 5317380 (63.42%) aligned exactly 1 time 2656493 (31.69%) aligned >1 times 95.11% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 829690 / 7973873 = 0.1041 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 09:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.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 09:06:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:06:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:06:55: 1000000 INFO @ Sat, 11 Dec 2021 09:07:00: 2000000 INFO @ Sat, 11 Dec 2021 09:07:06: 3000000 INFO @ Sat, 11 Dec 2021 09:07:11: 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 @ Sat, 11 Dec 2021 09:07:17: 5000000 INFO @ Sat, 11 Dec 2021 09:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.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 09:07:18: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:18: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:23: 6000000 INFO @ Sat, 11 Dec 2021 09:07:24: 1000000 INFO @ Sat, 11 Dec 2021 09:07:30: 7000000 INFO @ Sat, 11 Dec 2021 09:07:30: 2000000 INFO @ Sat, 11 Dec 2021 09:07:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:31: #1 total tags in treatment: 7144183 INFO @ Sat, 11 Dec 2021 09:07:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:31: #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 09:07:31: #1 tags after filtering in treatment: 7144181 INFO @ Sat, 11 Dec 2021 09:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:31: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:32: #2 number of paired peaks: 456 WARNING @ Sat, 11 Dec 2021 09:07:32: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:32: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:32: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:32: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:32: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:32: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:07:32: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.05_model.r WARNING @ Sat, 11 Dec 2021 09:07:32: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:32: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:07:32: #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 09:07:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:35: 3000000 INFO @ Sat, 11 Dec 2021 09:07:40: 4000000 INFO @ Sat, 11 Dec 2021 09:07:45: 5000000 INFO @ Sat, 11 Dec 2021 09:07:46: #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 @ Sat, 11 Dec 2021 09:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.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 09:07:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:07:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:07:51: 6000000 INFO @ Sat, 11 Dec 2021 09:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.05_summits.bed INFO @ Sat, 11 Dec 2021 09:07:53: Done! pass1 - making usageList (670 chroms): 1 millis pass2 - checking and writing primary data (1843 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:07:54: 1000000 INFO @ Sat, 11 Dec 2021 09:07:57: 7000000 INFO @ Sat, 11 Dec 2021 09:07:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:07:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:07:58: #1 total tags in treatment: 7144183 INFO @ Sat, 11 Dec 2021 09:07:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:07:58: #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 09:07:58: #1 tags after filtering in treatment: 7144181 INFO @ Sat, 11 Dec 2021 09:07:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:07:58: #1 finished! INFO @ Sat, 11 Dec 2021 09:07:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:07:59: #2 number of paired peaks: 456 WARNING @ Sat, 11 Dec 2021 09:07:59: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 11 Dec 2021 09:07:59: start model_add_line... INFO @ Sat, 11 Dec 2021 09:07:59: start X-correlation... INFO @ Sat, 11 Dec 2021 09:07:59: end of X-cor INFO @ Sat, 11 Dec 2021 09:07:59: #2 finished! INFO @ Sat, 11 Dec 2021 09:07:59: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:07:59: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.10_model.r WARNING @ Sat, 11 Dec 2021 09:07:59: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:07:59: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:07:59: #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 09:07:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:07:59: 2000000 INFO @ Sat, 11 Dec 2021 09:08:04: 3000000 INFO @ Sat, 11 Dec 2021 09:08:10: 4000000 INFO @ Sat, 11 Dec 2021 09:08:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:15: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:08:20: 6000000 INFO @ Sat, 11 Dec 2021 09:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.10_summits.bed INFO @ Sat, 11 Dec 2021 09:08:21: Done! pass1 - making usageList (344 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:08:26: 7000000 INFO @ Sat, 11 Dec 2021 09:08:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:08:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:08:27: #1 total tags in treatment: 7144183 INFO @ Sat, 11 Dec 2021 09:08:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:08:27: #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 09:08:27: #1 tags after filtering in treatment: 7144181 INFO @ Sat, 11 Dec 2021 09:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:08:27: #1 finished! INFO @ Sat, 11 Dec 2021 09:08:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:08:28: #2 number of paired peaks: 456 WARNING @ Sat, 11 Dec 2021 09:08:28: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sat, 11 Dec 2021 09:08:28: start model_add_line... INFO @ Sat, 11 Dec 2021 09:08:28: start X-correlation... INFO @ Sat, 11 Dec 2021 09:08:28: end of X-cor INFO @ Sat, 11 Dec 2021 09:08:28: #2 finished! INFO @ Sat, 11 Dec 2021 09:08:28: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 09:08:28: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Dec 2021 09:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.20_model.r WARNING @ Sat, 11 Dec 2021 09:08:28: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:08:28: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Dec 2021 09:08:28: #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 09:08:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:08:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:08:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689084/SRX8689084.20_summits.bed INFO @ Sat, 11 Dec 2021 09:08:50: Done! pass1 - making usageList (135 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 6 millis CompletedMACS2peakCalling