Job ID = 16439166 SRX = SRX15206438 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: 00:12:29 22813199 reads; of these: 22813199 (100.00%) were unpaired; of these: 520074 (2.28%) aligned 0 times 18891509 (82.81%) aligned exactly 1 time 3401616 (14.91%) aligned >1 times 97.72% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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 12 files... [bam_rmdupse_core] 2022588 / 22293125 = 0.0907 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:04:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.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 @ Tue, 02 Aug 2022 15:04:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:04:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:22: 1000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.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 @ Tue, 02 Aug 2022 15:04:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:04:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:04:36: 2000000 INFO @ Tue, 02 Aug 2022 15:04:51: 3000000 INFO @ Tue, 02 Aug 2022 15:04:52: 1000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:05:05: 4000000 INFO @ Tue, 02 Aug 2022 15:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.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 @ Tue, 02 Aug 2022 15:05:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:05:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:05:08: 2000000 INFO @ Tue, 02 Aug 2022 15:05:20: 5000000 INFO @ Tue, 02 Aug 2022 15:05:20: 1000000 INFO @ Tue, 02 Aug 2022 15:05:24: 3000000 INFO @ Tue, 02 Aug 2022 15:05:35: 2000000 INFO @ Tue, 02 Aug 2022 15:05:35: 6000000 INFO @ Tue, 02 Aug 2022 15:05:40: 4000000 INFO @ Tue, 02 Aug 2022 15:05:50: 3000000 INFO @ Tue, 02 Aug 2022 15:05:50: 7000000 INFO @ Tue, 02 Aug 2022 15:05:57: 5000000 INFO @ Tue, 02 Aug 2022 15:06:04: 4000000 INFO @ Tue, 02 Aug 2022 15:06:05: 8000000 INFO @ Tue, 02 Aug 2022 15:06:13: 6000000 INFO @ Tue, 02 Aug 2022 15:06:19: 5000000 INFO @ Tue, 02 Aug 2022 15:06:21: 9000000 INFO @ Tue, 02 Aug 2022 15:06:31: 7000000 INFO @ Tue, 02 Aug 2022 15:06:34: 6000000 INFO @ Tue, 02 Aug 2022 15:06:37: 10000000 INFO @ Tue, 02 Aug 2022 15:06:47: 8000000 INFO @ Tue, 02 Aug 2022 15:06:49: 7000000 INFO @ Tue, 02 Aug 2022 15:06:53: 11000000 INFO @ Tue, 02 Aug 2022 15:07:03: 9000000 INFO @ Tue, 02 Aug 2022 15:07:04: 8000000 INFO @ Tue, 02 Aug 2022 15:07:08: 12000000 INFO @ Tue, 02 Aug 2022 15:07:19: 10000000 INFO @ Tue, 02 Aug 2022 15:07:20: 9000000 INFO @ Tue, 02 Aug 2022 15:07:24: 13000000 INFO @ Tue, 02 Aug 2022 15:07:34: 11000000 INFO @ Tue, 02 Aug 2022 15:07:35: 10000000 INFO @ Tue, 02 Aug 2022 15:07:39: 14000000 INFO @ Tue, 02 Aug 2022 15:07:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:07:50: 11000000 INFO @ Tue, 02 Aug 2022 15:07:55: 15000000 INFO @ Tue, 02 Aug 2022 15:08:02: 13000000 INFO @ Tue, 02 Aug 2022 15:08:05: 12000000 INFO @ Tue, 02 Aug 2022 15:08:10: 16000000 INFO @ Tue, 02 Aug 2022 15:08:16: 14000000 INFO @ Tue, 02 Aug 2022 15:08:20: 13000000 INFO @ Tue, 02 Aug 2022 15:08:27: 17000000 INFO @ Tue, 02 Aug 2022 15:08:31: 15000000 INFO @ Tue, 02 Aug 2022 15:08:35: 14000000 INFO @ Tue, 02 Aug 2022 15:08:42: 18000000 INFO @ Tue, 02 Aug 2022 15:08:46: 16000000 INFO @ Tue, 02 Aug 2022 15:08:50: 15000000 INFO @ Tue, 02 Aug 2022 15:08:57: 19000000 INFO @ Tue, 02 Aug 2022 15:09:01: 17000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:09:06: 16000000 INFO @ Tue, 02 Aug 2022 15:09:12: 20000000 INFO @ Tue, 02 Aug 2022 15:09:16: 18000000 INFO @ Tue, 02 Aug 2022 15:09:17: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 15:09:17: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 15:09:17: #1 total tags in treatment: 20270537 INFO @ Tue, 02 Aug 2022 15:09:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:09:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:09:17: #1 tags after filtering in treatment: 20270388 INFO @ Tue, 02 Aug 2022 15:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:09:17: #1 finished! INFO @ Tue, 02 Aug 2022 15:09:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:09:19: #2 number of paired peaks: 167 WARNING @ Tue, 02 Aug 2022 15:09:19: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Tue, 02 Aug 2022 15:09:19: start model_add_line... INFO @ Tue, 02 Aug 2022 15:09:19: start X-correlation... INFO @ Tue, 02 Aug 2022 15:09:19: end of X-cor INFO @ Tue, 02 Aug 2022 15:09:19: #2 finished! INFO @ Tue, 02 Aug 2022 15:09:19: #2 predicted fragment length is 178 bps INFO @ Tue, 02 Aug 2022 15:09:19: #2 alternative fragment length(s) may be 3,154,170,178 bps INFO @ Tue, 02 Aug 2022 15:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.05_model.r WARNING @ Tue, 02 Aug 2022 15:09:19: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:09:19: #2 You may need to consider one of the other alternative d(s): 3,154,170,178 WARNING @ Tue, 02 Aug 2022 15:09:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:09:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:09:21: 17000000 INFO @ Tue, 02 Aug 2022 15:09:31: 19000000 INFO @ Tue, 02 Aug 2022 15:09:36: 18000000 INFO @ Tue, 02 Aug 2022 15:09:45: 20000000 INFO @ Tue, 02 Aug 2022 15:09:49: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 15:09:49: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 15:09:49: #1 total tags in treatment: 20270537 INFO @ Tue, 02 Aug 2022 15:09:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:09:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:09:50: 19000000 INFO @ Tue, 02 Aug 2022 15:09:50: #1 tags after filtering in treatment: 20270388 INFO @ Tue, 02 Aug 2022 15:09:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:09:50: #1 finished! INFO @ Tue, 02 Aug 2022 15:09:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:09:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:09:52: #2 number of paired peaks: 167 WARNING @ Tue, 02 Aug 2022 15:09:52: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Tue, 02 Aug 2022 15:09:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:09:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:09:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:09:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:09:52: #2 predicted fragment length is 178 bps INFO @ Tue, 02 Aug 2022 15:09:52: #2 alternative fragment length(s) may be 3,154,170,178 bps INFO @ Tue, 02 Aug 2022 15:09:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.10_model.r WARNING @ Tue, 02 Aug 2022 15:09:52: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:09:52: #2 You may need to consider one of the other alternative d(s): 3,154,170,178 WARNING @ Tue, 02 Aug 2022 15:09:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:09:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:09:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:10:03: 20000000 INFO @ Tue, 02 Aug 2022 15:10:07: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 15:10:07: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 15:10:07: #1 total tags in treatment: 20270537 INFO @ Tue, 02 Aug 2022 15:10:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:10:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:10:08: #1 tags after filtering in treatment: 20270388 INFO @ Tue, 02 Aug 2022 15:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:10:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:10:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:10:10: #2 number of paired peaks: 167 WARNING @ Tue, 02 Aug 2022 15:10:10: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Tue, 02 Aug 2022 15:10:10: start model_add_line... INFO @ Tue, 02 Aug 2022 15:10:10: start X-correlation... INFO @ Tue, 02 Aug 2022 15:10:10: end of X-cor INFO @ Tue, 02 Aug 2022 15:10:10: #2 finished! INFO @ Tue, 02 Aug 2022 15:10:10: #2 predicted fragment length is 178 bps INFO @ Tue, 02 Aug 2022 15:10:10: #2 alternative fragment length(s) may be 3,154,170,178 bps INFO @ Tue, 02 Aug 2022 15:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.20_model.r WARNING @ Tue, 02 Aug 2022 15:10:10: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:10:10: #2 You may need to consider one of the other alternative d(s): 3,154,170,178 WARNING @ Tue, 02 Aug 2022 15:10:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:10:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:10:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.05_summits.bed INFO @ Tue, 02 Aug 2022 15:10:36: Done! pass1 - making usageList (323 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:10:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:11:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.10_summits.bed INFO @ Tue, 02 Aug 2022 15:11:09: Done! pass1 - making usageList (245 chroms): 2 millis pass2 - checking and writing primary data (506 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:11:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206438/SRX15206438.20_summits.bed INFO @ Tue, 02 Aug 2022 15:11:24: Done! pass1 - making usageList (128 chroms): 2 millis pass2 - checking and writing primary data (223 records, 4 fields): 30 millis CompletedMACS2peakCalling