Job ID = 14170762 SRX = SRX8689108 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: 00:05:25 15640097 reads; of these: 15640097 (100.00%) were unpaired; of these: 502565 (3.21%) aligned 0 times 10331944 (66.06%) aligned exactly 1 time 4805588 (30.73%) aligned >1 times 96.79% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1962300 / 15137532 = 0.1296 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 08:36:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.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 08:36:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:36:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:36:51: 1000000 INFO @ Sat, 11 Dec 2021 08:36:58: 2000000 INFO @ Sat, 11 Dec 2021 08:37:04: 3000000 INFO @ Sat, 11 Dec 2021 08:37:11: 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 08:37:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.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 08:37:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:37:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:37:18: 5000000 INFO @ Sat, 11 Dec 2021 08:37:22: 1000000 INFO @ Sat, 11 Dec 2021 08:37:25: 6000000 INFO @ Sat, 11 Dec 2021 08:37:29: 2000000 INFO @ Sat, 11 Dec 2021 08:37:33: 7000000 INFO @ Sat, 11 Dec 2021 08:37:36: 3000000 INFO @ Sat, 11 Dec 2021 08:37:40: 8000000 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 08:37:43: 4000000 INFO @ Sat, 11 Dec 2021 08:37:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.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 08:37:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:37:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:37:47: 9000000 INFO @ Sat, 11 Dec 2021 08:37:51: 5000000 INFO @ Sat, 11 Dec 2021 08:37:53: 1000000 INFO @ Sat, 11 Dec 2021 08:37:55: 10000000 INFO @ Sat, 11 Dec 2021 08:37:58: 6000000 INFO @ Sat, 11 Dec 2021 08:38:01: 2000000 INFO @ Sat, 11 Dec 2021 08:38:03: 11000000 INFO @ Sat, 11 Dec 2021 08:38:06: 7000000 INFO @ Sat, 11 Dec 2021 08:38:09: 3000000 INFO @ Sat, 11 Dec 2021 08:38:11: 12000000 INFO @ Sat, 11 Dec 2021 08:38:14: 8000000 INFO @ Sat, 11 Dec 2021 08:38:16: 4000000 INFO @ Sat, 11 Dec 2021 08:38:19: 13000000 INFO @ Sat, 11 Dec 2021 08:38:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:38:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:38:20: #1 total tags in treatment: 13175232 INFO @ Sat, 11 Dec 2021 08:38:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:38:20: #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 08:38:21: 9000000 INFO @ Sat, 11 Dec 2021 08:38:21: #1 tags after filtering in treatment: 13175231 INFO @ Sat, 11 Dec 2021 08:38:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:38:21: #1 finished! INFO @ Sat, 11 Dec 2021 08:38:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:38:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:38:22: #2 number of paired peaks: 362 WARNING @ Sat, 11 Dec 2021 08:38:22: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 11 Dec 2021 08:38:22: start model_add_line... INFO @ Sat, 11 Dec 2021 08:38:22: start X-correlation... INFO @ Sat, 11 Dec 2021 08:38:22: end of X-cor INFO @ Sat, 11 Dec 2021 08:38:22: #2 finished! INFO @ Sat, 11 Dec 2021 08:38:22: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 08:38:22: #2 alternative fragment length(s) may be 4,52,549 bps INFO @ Sat, 11 Dec 2021 08:38:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.05_model.r WARNING @ Sat, 11 Dec 2021 08:38:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:38:22: #2 You may need to consider one of the other alternative d(s): 4,52,549 WARNING @ Sat, 11 Dec 2021 08:38:22: #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 08:38:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:38:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:38:24: 5000000 INFO @ Sat, 11 Dec 2021 08:38:28: 10000000 INFO @ Sat, 11 Dec 2021 08:38:31: 6000000 INFO @ Sat, 11 Dec 2021 08:38:36: 11000000 INFO @ Sat, 11 Dec 2021 08:38:38: 7000000 INFO @ Sat, 11 Dec 2021 08:38:43: 12000000 INFO @ Sat, 11 Dec 2021 08:38:45: 8000000 INFO @ Sat, 11 Dec 2021 08:38:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:38:50: 13000000 INFO @ Sat, 11 Dec 2021 08:38:51: 9000000 INFO @ Sat, 11 Dec 2021 08:38:52: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:38:52: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:38:52: #1 total tags in treatment: 13175232 INFO @ Sat, 11 Dec 2021 08:38:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:38:52: #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 08:38:53: #1 tags after filtering in treatment: 13175231 INFO @ Sat, 11 Dec 2021 08:38:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:38:53: #1 finished! INFO @ Sat, 11 Dec 2021 08:38:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:38:54: #2 number of paired peaks: 362 WARNING @ Sat, 11 Dec 2021 08:38:54: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 11 Dec 2021 08:38:54: start model_add_line... INFO @ Sat, 11 Dec 2021 08:38:54: start X-correlation... INFO @ Sat, 11 Dec 2021 08:38:54: end of X-cor INFO @ Sat, 11 Dec 2021 08:38:54: #2 finished! INFO @ Sat, 11 Dec 2021 08:38:54: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 08:38:54: #2 alternative fragment length(s) may be 4,52,549 bps INFO @ Sat, 11 Dec 2021 08:38:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.10_model.r WARNING @ Sat, 11 Dec 2021 08:38:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:38:54: #2 You may need to consider one of the other alternative d(s): 4,52,549 WARNING @ Sat, 11 Dec 2021 08:38:54: #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 08:38:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:38:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:38:58: 10000000 INFO @ Sat, 11 Dec 2021 08:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.05_summits.bed INFO @ Sat, 11 Dec 2021 08:39:02: Done! pass1 - making usageList (729 chroms): 2 millis pass2 - checking and writing primary data (2629 records, 4 fields): 47 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:39:06: 11000000 INFO @ Sat, 11 Dec 2021 08:39:12: 12000000 INFO @ Sat, 11 Dec 2021 08:39:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:39:19: 13000000 INFO @ Sat, 11 Dec 2021 08:39:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:39:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:39:20: #1 total tags in treatment: 13175232 INFO @ Sat, 11 Dec 2021 08:39:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:39:20: #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 08:39:21: #1 tags after filtering in treatment: 13175231 INFO @ Sat, 11 Dec 2021 08:39:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:39:21: #1 finished! INFO @ Sat, 11 Dec 2021 08:39:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:39:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:39:22: #2 number of paired peaks: 362 WARNING @ Sat, 11 Dec 2021 08:39:22: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Sat, 11 Dec 2021 08:39:22: start model_add_line... INFO @ Sat, 11 Dec 2021 08:39:22: start X-correlation... INFO @ Sat, 11 Dec 2021 08:39:22: end of X-cor INFO @ Sat, 11 Dec 2021 08:39:22: #2 finished! INFO @ Sat, 11 Dec 2021 08:39:22: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 08:39:22: #2 alternative fragment length(s) may be 4,52,549 bps INFO @ Sat, 11 Dec 2021 08:39:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.20_model.r WARNING @ Sat, 11 Dec 2021 08:39:22: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:39:22: #2 You may need to consider one of the other alternative d(s): 4,52,549 WARNING @ Sat, 11 Dec 2021 08:39:22: #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 08:39:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:39:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:39:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:39:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:39:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.10_summits.bed INFO @ Sat, 11 Dec 2021 08:39:33: Done! pass1 - making usageList (428 chroms): 1 millis pass2 - checking and writing primary data (1126 records, 4 fields): 29 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:39:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:40:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:40:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689108/SRX8689108.20_summits.bed INFO @ Sat, 11 Dec 2021 08:40:01: Done! pass1 - making usageList (187 chroms): 1 millis pass2 - checking and writing primary data (380 records, 4 fields): 14 millis CompletedMACS2peakCalling