Job ID = 14171309 SRX = SRX9986141 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27285086 spots for SRR13591504/SRR13591504.sra Written 27285086 spots for SRR13591504/SRR13591504.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171763 ("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: 00:09:32 27285086 reads; of these: 27285086 (100.00%) were unpaired; of these: 1136129 (4.16%) aligned 0 times 15842163 (58.06%) aligned exactly 1 time 10306794 (37.77%) aligned >1 times 95.84% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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 12 files... [bam_rmdupse_core] 6180582 / 26148957 = 0.2364 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 11:20:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.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 11:20:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:20:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:20:51: 1000000 INFO @ Sat, 11 Dec 2021 11:20:58: 2000000 INFO @ Sat, 11 Dec 2021 11:21:04: 3000000 INFO @ Sat, 11 Dec 2021 11:21:11: 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 11:21:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.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 11:21:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:21:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:21:18: 5000000 INFO @ Sat, 11 Dec 2021 11:21:22: 1000000 INFO @ Sat, 11 Dec 2021 11:21:25: 6000000 INFO @ Sat, 11 Dec 2021 11:21:30: 2000000 INFO @ Sat, 11 Dec 2021 11:21:32: 7000000 INFO @ Sat, 11 Dec 2021 11:21:37: 3000000 INFO @ Sat, 11 Dec 2021 11:21:39: 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 11:21:44: 4000000 INFO @ Sat, 11 Dec 2021 11:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.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 11:21:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:21:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:21:46: 9000000 INFO @ Sat, 11 Dec 2021 11:21:51: 5000000 INFO @ Sat, 11 Dec 2021 11:21:52: 1000000 INFO @ Sat, 11 Dec 2021 11:21:53: 10000000 INFO @ Sat, 11 Dec 2021 11:21:58: 6000000 INFO @ Sat, 11 Dec 2021 11:21:59: 2000000 INFO @ Sat, 11 Dec 2021 11:22:01: 11000000 INFO @ Sat, 11 Dec 2021 11:22:06: 7000000 INFO @ Sat, 11 Dec 2021 11:22:06: 3000000 INFO @ Sat, 11 Dec 2021 11:22:08: 12000000 INFO @ Sat, 11 Dec 2021 11:22:13: 8000000 INFO @ Sat, 11 Dec 2021 11:22:13: 4000000 INFO @ Sat, 11 Dec 2021 11:22:15: 13000000 INFO @ Sat, 11 Dec 2021 11:22:20: 9000000 INFO @ Sat, 11 Dec 2021 11:22:21: 5000000 INFO @ Sat, 11 Dec 2021 11:22:22: 14000000 INFO @ Sat, 11 Dec 2021 11:22:28: 10000000 INFO @ Sat, 11 Dec 2021 11:22:28: 6000000 INFO @ Sat, 11 Dec 2021 11:22:29: 15000000 INFO @ Sat, 11 Dec 2021 11:22:35: 11000000 INFO @ Sat, 11 Dec 2021 11:22:36: 7000000 INFO @ Sat, 11 Dec 2021 11:22:36: 16000000 INFO @ Sat, 11 Dec 2021 11:22:42: 12000000 INFO @ Sat, 11 Dec 2021 11:22:43: 8000000 INFO @ Sat, 11 Dec 2021 11:22:44: 17000000 INFO @ Sat, 11 Dec 2021 11:22:50: 13000000 INFO @ Sat, 11 Dec 2021 11:22:50: 9000000 INFO @ Sat, 11 Dec 2021 11:22:51: 18000000 INFO @ Sat, 11 Dec 2021 11:22:57: 14000000 INFO @ Sat, 11 Dec 2021 11:22:57: 10000000 INFO @ Sat, 11 Dec 2021 11:22:58: 19000000 INFO @ Sat, 11 Dec 2021 11:23:04: 15000000 INFO @ Sat, 11 Dec 2021 11:23:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:23:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:23:05: #1 total tags in treatment: 19968375 INFO @ Sat, 11 Dec 2021 11:23:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:23:05: #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 11:23:05: 11000000 INFO @ Sat, 11 Dec 2021 11:23:05: #1 tags after filtering in treatment: 19968375 INFO @ Sat, 11 Dec 2021 11:23:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:23:05: #1 finished! INFO @ Sat, 11 Dec 2021 11:23:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:23:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:23:06: #2 number of paired peaks: 190 WARNING @ Sat, 11 Dec 2021 11:23:06: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sat, 11 Dec 2021 11:23:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:23:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:23:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:23:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:23:06: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 11:23:06: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 11 Dec 2021 11:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.05_model.r WARNING @ Sat, 11 Dec 2021 11:23:06: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:23:06: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 11 Dec 2021 11:23:06: #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 11:23:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:23:10: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:23:12: 12000000 INFO @ Sat, 11 Dec 2021 11:23:17: 17000000 INFO @ Sat, 11 Dec 2021 11:23:19: 13000000 INFO @ Sat, 11 Dec 2021 11:23:25: 18000000 INFO @ Sat, 11 Dec 2021 11:23:26: 14000000 INFO @ Sat, 11 Dec 2021 11:23:31: 19000000 INFO @ Sat, 11 Dec 2021 11:23:33: 15000000 INFO @ Sat, 11 Dec 2021 11:23:38: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:23:38: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:23:38: #1 total tags in treatment: 19968375 INFO @ Sat, 11 Dec 2021 11:23:38: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:23:38: #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 11:23:38: #1 tags after filtering in treatment: 19968375 INFO @ Sat, 11 Dec 2021 11:23:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:23:38: #1 finished! INFO @ Sat, 11 Dec 2021 11:23:38: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:23:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:23:39: #2 number of paired peaks: 190 WARNING @ Sat, 11 Dec 2021 11:23:39: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sat, 11 Dec 2021 11:23:39: start model_add_line... INFO @ Sat, 11 Dec 2021 11:23:39: start X-correlation... INFO @ Sat, 11 Dec 2021 11:23:39: end of X-cor INFO @ Sat, 11 Dec 2021 11:23:39: #2 finished! INFO @ Sat, 11 Dec 2021 11:23:39: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 11:23:39: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 11 Dec 2021 11:23:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.10_model.r WARNING @ Sat, 11 Dec 2021 11:23:39: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:23:39: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 11 Dec 2021 11:23:39: #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 11:23:39: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:23:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:23:40: 16000000 INFO @ Sat, 11 Dec 2021 11:23:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:23:46: 17000000 INFO @ Sat, 11 Dec 2021 11:23:52: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:23:58: 19000000 INFO @ Sat, 11 Dec 2021 11:24:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:24:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:24:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.05_summits.bed INFO @ Sat, 11 Dec 2021 11:24:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3194 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:24:04: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 11:24:04: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 11:24:04: #1 total tags in treatment: 19968375 INFO @ Sat, 11 Dec 2021 11:24:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:24:04: #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 11:24:05: #1 tags after filtering in treatment: 19968375 INFO @ Sat, 11 Dec 2021 11:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:24:05: #1 finished! INFO @ Sat, 11 Dec 2021 11:24:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:24:06: #2 number of paired peaks: 190 WARNING @ Sat, 11 Dec 2021 11:24:06: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sat, 11 Dec 2021 11:24:06: start model_add_line... INFO @ Sat, 11 Dec 2021 11:24:06: start X-correlation... INFO @ Sat, 11 Dec 2021 11:24:06: end of X-cor INFO @ Sat, 11 Dec 2021 11:24:06: #2 finished! INFO @ Sat, 11 Dec 2021 11:24:06: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 11:24:06: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 11 Dec 2021 11:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.20_model.r WARNING @ Sat, 11 Dec 2021 11:24:06: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:24:06: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 11 Dec 2021 11:24:06: #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 11:24:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:24:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:24:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:24:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:24:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.10_summits.bed INFO @ Sat, 11 Dec 2021 11:24:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2048 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:24:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:24:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:24:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:24:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9986141/SRX9986141.20_summits.bed INFO @ Sat, 11 Dec 2021 11:24:59: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (851 records, 4 fields): 2 millis CompletedMACS2peakCalling