Job ID = 14171358 SRX = SRX8512933 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11274144 spots for SRR11969179/SRR11969179.sra Written 11274144 spots for SRR11969179/SRR11969179.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171844 ("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: 00:07:53 11274144 reads; of these: 11274144 (100.00%) were unpaired; of these: 1575 (0.01%) aligned 0 times 9761252 (86.58%) aligned exactly 1 time 1511317 (13.41%) aligned >1 times 99.99% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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 8 files... [bam_rmdupse_core] 947572 / 11272569 = 0.0841 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 11:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.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 11:40:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:27: 1000000 INFO @ Sat, 11 Dec 2021 11:40:37: 2000000 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 11:40:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.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 11:40:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:40:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:40:47: 3000000 INFO @ Sat, 11 Dec 2021 11:40:57: 4000000 INFO @ Sat, 11 Dec 2021 11:40:57: 1000000 INFO @ Sat, 11 Dec 2021 11:41:07: 5000000 INFO @ Sat, 11 Dec 2021 11:41:08: 2000000 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 11:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.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 11:41:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:41:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:41:18: 6000000 INFO @ Sat, 11 Dec 2021 11:41:19: 3000000 INFO @ Sat, 11 Dec 2021 11:41:29: 7000000 INFO @ Sat, 11 Dec 2021 11:41:29: 4000000 INFO @ Sat, 11 Dec 2021 11:41:31: 1000000 INFO @ Sat, 11 Dec 2021 11:41:40: 8000000 INFO @ Sat, 11 Dec 2021 11:41:40: 5000000 INFO @ Sat, 11 Dec 2021 11:41:44: 2000000 INFO @ Sat, 11 Dec 2021 11:41:52: 6000000 INFO @ Sat, 11 Dec 2021 11:41:53: 9000000 INFO @ Sat, 11 Dec 2021 11:41:58: 3000000 INFO @ Sat, 11 Dec 2021 11:42:03: 7000000 INFO @ Sat, 11 Dec 2021 11:42:04: 10000000 INFO @ Sat, 11 Dec 2021 11:42:07: #1 tag size is determined as 140 bps INFO @ Sat, 11 Dec 2021 11:42:07: #1 tag size = 140 INFO @ Sat, 11 Dec 2021 11:42:07: #1 total tags in treatment: 10324997 INFO @ Sat, 11 Dec 2021 11:42:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:07: #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 11:42:08: #1 tags after filtering in treatment: 10324997 INFO @ Sat, 11 Dec 2021 11:42:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:42:08: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:09: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 11:42:09: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 11:42:09: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:09: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:09: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:09: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:09: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 11:42:09: #2 alternative fragment length(s) may be 4,145,576 bps INFO @ Sat, 11 Dec 2021 11:42:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.05_model.r WARNING @ Sat, 11 Dec 2021 11:42:09: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:42:09: #2 You may need to consider one of the other alternative d(s): 4,145,576 WARNING @ Sat, 11 Dec 2021 11:42:09: #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 11:42:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:10: 4000000 INFO @ Sat, 11 Dec 2021 11:42:13: 8000000 INFO @ Sat, 11 Dec 2021 11:42:24: 5000000 INFO @ Sat, 11 Dec 2021 11:42:27: 9000000 INFO @ Sat, 11 Dec 2021 11:42:39: 6000000 INFO @ Sat, 11 Dec 2021 11:42:40: 10000000 INFO @ Sat, 11 Dec 2021 11:42:43: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:42:45: #1 tag size is determined as 140 bps INFO @ Sat, 11 Dec 2021 11:42:45: #1 tag size = 140 INFO @ Sat, 11 Dec 2021 11:42:45: #1 total tags in treatment: 10324997 INFO @ Sat, 11 Dec 2021 11:42:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:42:45: #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 11:42:45: #1 tags after filtering in treatment: 10324997 INFO @ Sat, 11 Dec 2021 11:42:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:42:45: #1 finished! INFO @ Sat, 11 Dec 2021 11:42:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:42:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:42:46: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 11:42:46: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 11:42:46: start model_add_line... INFO @ Sat, 11 Dec 2021 11:42:46: start X-correlation... INFO @ Sat, 11 Dec 2021 11:42:46: end of X-cor INFO @ Sat, 11 Dec 2021 11:42:46: #2 finished! INFO @ Sat, 11 Dec 2021 11:42:46: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 11:42:46: #2 alternative fragment length(s) may be 4,145,576 bps INFO @ Sat, 11 Dec 2021 11:42:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.10_model.r WARNING @ Sat, 11 Dec 2021 11:42:46: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:42:46: #2 You may need to consider one of the other alternative d(s): 4,145,576 WARNING @ Sat, 11 Dec 2021 11:42:46: #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 11:42:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:42:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:42:53: 7000000 INFO @ Sat, 11 Dec 2021 11:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.05_summits.bed INFO @ Sat, 11 Dec 2021 11:43:01: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3504 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:43:06: 8000000 INFO @ Sat, 11 Dec 2021 11:43:20: 9000000 INFO @ Sat, 11 Dec 2021 11:43:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:43:32: 10000000 INFO @ Sat, 11 Dec 2021 11:43:37: #1 tag size is determined as 140 bps INFO @ Sat, 11 Dec 2021 11:43:37: #1 tag size = 140 INFO @ Sat, 11 Dec 2021 11:43:37: #1 total tags in treatment: 10324997 INFO @ Sat, 11 Dec 2021 11:43:37: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:43:37: #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 11:43:37: #1 tags after filtering in treatment: 10324997 INFO @ Sat, 11 Dec 2021 11:43:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:43:37: #1 finished! INFO @ Sat, 11 Dec 2021 11:43:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:43:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:43:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:43:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:43:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.10_summits.bed INFO @ Sat, 11 Dec 2021 11:43:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:43:38: #2 number of paired peaks: 161 WARNING @ Sat, 11 Dec 2021 11:43:38: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 11 Dec 2021 11:43:38: start model_add_line... INFO @ Sat, 11 Dec 2021 11:43:38: start X-correlation... INFO @ Sat, 11 Dec 2021 11:43:38: end of X-cor INFO @ Sat, 11 Dec 2021 11:43:38: #2 finished! INFO @ Sat, 11 Dec 2021 11:43:38: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 11:43:38: #2 alternative fragment length(s) may be 4,145,576 bps INFO @ Sat, 11 Dec 2021 11:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.20_model.r WARNING @ Sat, 11 Dec 2021 11:43:38: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:43:38: #2 You may need to consider one of the other alternative d(s): 4,145,576 WARNING @ Sat, 11 Dec 2021 11:43:38: #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 11:43:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:43:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:44:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512933/SRX8512933.20_summits.bed INFO @ Sat, 11 Dec 2021 11:44:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 2 millis CompletedMACS2peakCalling