Job ID = 12265284 SRX = SRX5010743 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 47304001 spots for SRR8191168/SRR8191168.sra Written 47304001 spots for SRR8191168/SRR8191168.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265470 ("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: 00:14:53 47304001 reads; of these: 47304001 (100.00%) were unpaired; of these: 1409386 (2.98%) aligned 0 times 18692347 (39.52%) aligned exactly 1 time 27202268 (57.51%) aligned >1 times 97.02% overall alignment rate Time searching: 00:14:53 Overall time: 00:14:53 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 20 files... [bam_rmdupse_core] 30005706 / 45894615 = 0.6538 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:51:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.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, 03 Apr 2021 06:51:01: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:51:01: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:51:08: 1000000 INFO @ Sat, 03 Apr 2021 06:51:16: 2000000 INFO @ Sat, 03 Apr 2021 06:51:24: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.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, 03 Apr 2021 06:51:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:51:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:51:32: 4000000 INFO @ Sat, 03 Apr 2021 06:51:39: 1000000 INFO @ Sat, 03 Apr 2021 06:51:41: 5000000 INFO @ Sat, 03 Apr 2021 06:51:47: 2000000 INFO @ Sat, 03 Apr 2021 06:51:48: 6000000 INFO @ Sat, 03 Apr 2021 06:51:55: 3000000 INFO @ Sat, 03 Apr 2021 06:51:56: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.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, 03 Apr 2021 06:52:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:52:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:52:04: 4000000 INFO @ Sat, 03 Apr 2021 06:52:05: 8000000 INFO @ Sat, 03 Apr 2021 06:52:11: 1000000 INFO @ Sat, 03 Apr 2021 06:52:13: 9000000 INFO @ Sat, 03 Apr 2021 06:52:13: 5000000 INFO @ Sat, 03 Apr 2021 06:52:21: 10000000 INFO @ Sat, 03 Apr 2021 06:52:22: 6000000 INFO @ Sat, 03 Apr 2021 06:52:22: 2000000 INFO @ Sat, 03 Apr 2021 06:52:30: 11000000 INFO @ Sat, 03 Apr 2021 06:52:30: 7000000 INFO @ Sat, 03 Apr 2021 06:52:34: 3000000 INFO @ Sat, 03 Apr 2021 06:52:38: 12000000 INFO @ Sat, 03 Apr 2021 06:52:39: 8000000 INFO @ Sat, 03 Apr 2021 06:52:44: 4000000 INFO @ Sat, 03 Apr 2021 06:52:47: 13000000 INFO @ Sat, 03 Apr 2021 06:52:48: 9000000 INFO @ Sat, 03 Apr 2021 06:52:55: 5000000 INFO @ Sat, 03 Apr 2021 06:52:55: 14000000 INFO @ Sat, 03 Apr 2021 06:52:57: 10000000 INFO @ Sat, 03 Apr 2021 06:53:03: 15000000 INFO @ Sat, 03 Apr 2021 06:53:05: 6000000 INFO @ Sat, 03 Apr 2021 06:53:06: 11000000 INFO @ Sat, 03 Apr 2021 06:53:11: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:53:11: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:53:11: #1 total tags in treatment: 15888909 INFO @ Sat, 03 Apr 2021 06:53:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:53:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:53:11: #1 tags after filtering in treatment: 15888909 INFO @ Sat, 03 Apr 2021 06:53:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:53:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:53:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:53:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:53:13: #2 number of paired peaks: 196 WARNING @ Sat, 03 Apr 2021 06:53:13: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Apr 2021 06:53:13: start model_add_line... INFO @ Sat, 03 Apr 2021 06:53:13: start X-correlation... INFO @ Sat, 03 Apr 2021 06:53:13: end of X-cor INFO @ Sat, 03 Apr 2021 06:53:13: #2 finished! INFO @ Sat, 03 Apr 2021 06:53:13: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 06:53:13: #2 alternative fragment length(s) may be 4,50,554 bps INFO @ Sat, 03 Apr 2021 06:53:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.05_model.r WARNING @ Sat, 03 Apr 2021 06:53:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:53:13: #2 You may need to consider one of the other alternative d(s): 4,50,554 WARNING @ Sat, 03 Apr 2021 06:53:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:53:13: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:53:15: 7000000 INFO @ Sat, 03 Apr 2021 06:53:15: 12000000 INFO @ Sat, 03 Apr 2021 06:53:24: 13000000 INFO @ Sat, 03 Apr 2021 06:53:25: 8000000 INFO @ Sat, 03 Apr 2021 06:53:33: 14000000 INFO @ Sat, 03 Apr 2021 06:53:35: 9000000 INFO @ Sat, 03 Apr 2021 06:53:42: 15000000 INFO @ Sat, 03 Apr 2021 06:53:45: 10000000 INFO @ Sat, 03 Apr 2021 06:53:50: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:53:50: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:53:50: #1 total tags in treatment: 15888909 INFO @ Sat, 03 Apr 2021 06:53:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:53:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:53:50: #1 tags after filtering in treatment: 15888909 INFO @ Sat, 03 Apr 2021 06:53:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:53:50: #1 finished! INFO @ Sat, 03 Apr 2021 06:53:50: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:53:52: #2 number of paired peaks: 196 WARNING @ Sat, 03 Apr 2021 06:53:52: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Apr 2021 06:53:52: start model_add_line... INFO @ Sat, 03 Apr 2021 06:53:52: start X-correlation... INFO @ Sat, 03 Apr 2021 06:53:52: end of X-cor INFO @ Sat, 03 Apr 2021 06:53:52: #2 finished! INFO @ Sat, 03 Apr 2021 06:53:52: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 06:53:52: #2 alternative fragment length(s) may be 4,50,554 bps INFO @ Sat, 03 Apr 2021 06:53:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.10_model.r WARNING @ Sat, 03 Apr 2021 06:53:52: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:53:52: #2 You may need to consider one of the other alternative d(s): 4,50,554 WARNING @ Sat, 03 Apr 2021 06:53:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:53:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:53:55: 11000000 INFO @ Sat, 03 Apr 2021 06:53:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:54:06: 12000000 INFO @ Sat, 03 Apr 2021 06:54:15: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:54:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:54:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.05_summits.bed INFO @ Sat, 03 Apr 2021 06:54:22: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9000 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:54:25: 14000000 INFO @ Sat, 03 Apr 2021 06:54:34: 15000000 INFO @ Sat, 03 Apr 2021 06:54:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:54:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:54:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:54:43: #1 total tags in treatment: 15888909 INFO @ Sat, 03 Apr 2021 06:54:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:54:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:54:43: #1 tags after filtering in treatment: 15888909 INFO @ Sat, 03 Apr 2021 06:54:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:54:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:54:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:54:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:54:44: #2 number of paired peaks: 196 WARNING @ Sat, 03 Apr 2021 06:54:44: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sat, 03 Apr 2021 06:54:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:54:45: start X-correlation... INFO @ Sat, 03 Apr 2021 06:54:45: end of X-cor INFO @ Sat, 03 Apr 2021 06:54:45: #2 finished! INFO @ Sat, 03 Apr 2021 06:54:45: #2 predicted fragment length is 50 bps INFO @ Sat, 03 Apr 2021 06:54:45: #2 alternative fragment length(s) may be 4,50,554 bps INFO @ Sat, 03 Apr 2021 06:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.20_model.r WARNING @ Sat, 03 Apr 2021 06:54:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:54:45: #2 You may need to consider one of the other alternative d(s): 4,50,554 WARNING @ Sat, 03 Apr 2021 06:54:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:54:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.10_summits.bed INFO @ Sat, 03 Apr 2021 06:55:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3486 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:55:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010743/SRX5010743.20_summits.bed INFO @ Sat, 03 Apr 2021 06:55:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 3 millis CompletedMACS2peakCalling