Job ID = 14170334 SRX = SRX8689105 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17564911 spots for SRR12174338/SRR12174338.sra Written 17564911 spots for SRR12174338/SRR12174338.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170794 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:15 17564911 reads; of these: 17564911 (100.00%) were unpaired; of these: 413483 (2.35%) aligned 0 times 12424110 (70.73%) aligned exactly 1 time 4727318 (26.91%) aligned >1 times 97.65% overall alignment rate Time searching: 00:21:15 Overall time: 00:21:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1307554 / 17151428 = 0.0762 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 06:45:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.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 06:45:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:27: 1000000 INFO @ Sat, 11 Dec 2021 06:45:32: 2000000 INFO @ Sat, 11 Dec 2021 06:45:36: 3000000 INFO @ Sat, 11 Dec 2021 06:45:41: 4000000 INFO @ Sat, 11 Dec 2021 06:45:46: 5000000 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 06:45:51: 6000000 INFO @ Sat, 11 Dec 2021 06:45:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.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 06:45:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:45:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:45:56: 7000000 INFO @ Sat, 11 Dec 2021 06:45:56: 1000000 INFO @ Sat, 11 Dec 2021 06:46:01: 8000000 INFO @ Sat, 11 Dec 2021 06:46:01: 2000000 INFO @ Sat, 11 Dec 2021 06:46:06: 3000000 INFO @ Sat, 11 Dec 2021 06:46:06: 9000000 INFO @ Sat, 11 Dec 2021 06:46:11: 4000000 INFO @ Sat, 11 Dec 2021 06:46:11: 10000000 INFO @ Sat, 11 Dec 2021 06:46:16: 5000000 INFO @ Sat, 11 Dec 2021 06:46:16: 11000000 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 06:46:20: 6000000 INFO @ Sat, 11 Dec 2021 06:46:21: 12000000 INFO @ Sat, 11 Dec 2021 06:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.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 06:46:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:46:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:46:25: 7000000 INFO @ Sat, 11 Dec 2021 06:46:26: 1000000 INFO @ Sat, 11 Dec 2021 06:46:26: 13000000 INFO @ Sat, 11 Dec 2021 06:46:30: 8000000 INFO @ Sat, 11 Dec 2021 06:46:31: 2000000 INFO @ Sat, 11 Dec 2021 06:46:31: 14000000 INFO @ Sat, 11 Dec 2021 06:46:35: 9000000 INFO @ Sat, 11 Dec 2021 06:46:36: 3000000 INFO @ Sat, 11 Dec 2021 06:46:36: 15000000 INFO @ Sat, 11 Dec 2021 06:46:40: 10000000 INFO @ Sat, 11 Dec 2021 06:46:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:46:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:46:41: #1 total tags in treatment: 15843874 INFO @ Sat, 11 Dec 2021 06:46:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:46:41: #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 06:46:41: 4000000 INFO @ Sat, 11 Dec 2021 06:46:41: #1 tags after filtering in treatment: 15843874 INFO @ Sat, 11 Dec 2021 06:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:46:41: #1 finished! INFO @ Sat, 11 Dec 2021 06:46:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:46:42: #2 number of paired peaks: 143 WARNING @ Sat, 11 Dec 2021 06:46:42: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 11 Dec 2021 06:46:42: start model_add_line... INFO @ Sat, 11 Dec 2021 06:46:42: start X-correlation... INFO @ Sat, 11 Dec 2021 06:46:42: end of X-cor INFO @ Sat, 11 Dec 2021 06:46:42: #2 finished! INFO @ Sat, 11 Dec 2021 06:46:42: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 06:46:42: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 11 Dec 2021 06:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.05_model.r WARNING @ Sat, 11 Dec 2021 06:46:42: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:46:42: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 11 Dec 2021 06:46:42: #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 06:46:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:46:45: 11000000 INFO @ Sat, 11 Dec 2021 06:46:45: 5000000 INFO @ Sat, 11 Dec 2021 06:46:50: 12000000 INFO @ Sat, 11 Dec 2021 06:46:50: 6000000 INFO @ Sat, 11 Dec 2021 06:46:54: 13000000 INFO @ Sat, 11 Dec 2021 06:46:55: 7000000 INFO @ Sat, 11 Dec 2021 06:46:59: 14000000 INFO @ Sat, 11 Dec 2021 06:47:00: 8000000 INFO @ Sat, 11 Dec 2021 06:47:04: 15000000 INFO @ Sat, 11 Dec 2021 06:47:05: 9000000 INFO @ Sat, 11 Dec 2021 06:47:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:08: #1 total tags in treatment: 15843874 INFO @ Sat, 11 Dec 2021 06:47:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:08: #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 06:47:08: #1 tags after filtering in treatment: 15843874 INFO @ Sat, 11 Dec 2021 06:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:08: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:09: #2 number of paired peaks: 143 WARNING @ Sat, 11 Dec 2021 06:47:09: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:09: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:09: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:09: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:09: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:09: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 06:47:09: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 11 Dec 2021 06:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.10_model.r WARNING @ Sat, 11 Dec 2021 06:47:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:09: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 11 Dec 2021 06:47:09: #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 06:47:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:09: 10000000 INFO @ Sat, 11 Dec 2021 06:47:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:14: 11000000 INFO @ Sat, 11 Dec 2021 06:47:19: 12000000 INFO @ Sat, 11 Dec 2021 06:47:23: 13000000 INFO @ Sat, 11 Dec 2021 06:47:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:47:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.05_summits.bed INFO @ Sat, 11 Dec 2021 06:47:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1690 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:47:28: 14000000 INFO @ Sat, 11 Dec 2021 06:47:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:47:37: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:37: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:37: #1 total tags in treatment: 15843874 INFO @ Sat, 11 Dec 2021 06:47:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:37: #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 06:47:37: #1 tags after filtering in treatment: 15843874 INFO @ Sat, 11 Dec 2021 06:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:37: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:47:38: #2 number of paired peaks: 143 WARNING @ Sat, 11 Dec 2021 06:47:38: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:38: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:38: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:38: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:38: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:38: #2 predicted fragment length is 46 bps INFO @ Sat, 11 Dec 2021 06:47:38: #2 alternative fragment length(s) may be 46 bps INFO @ Sat, 11 Dec 2021 06:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.20_model.r WARNING @ Sat, 11 Dec 2021 06:47:38: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:38: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Sat, 11 Dec 2021 06:47:38: #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 06:47:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.10_summits.bed INFO @ Sat, 11 Dec 2021 06:47:52: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1216 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689105/SRX8689105.20_summits.bed INFO @ Sat, 11 Dec 2021 06:48:21: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (927 records, 4 fields): 3 millis CompletedMACS2peakCalling