Job ID = 14168083 SRX = SRX8688977 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17493181 spots for SRR12174346/SRR12174346.sra Written 17493181 spots for SRR12174346/SRR12174346.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168845 ("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: 00:06:06 17493181 reads; of these: 17493181 (100.00%) were unpaired; of these: 409600 (2.34%) aligned 0 times 12159856 (69.51%) aligned exactly 1 time 4923725 (28.15%) aligned >1 times 97.66% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 1582026 / 17083581 = 0.0926 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 @ Fri, 10 Dec 2021 15:21:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.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 @ Fri, 10 Dec 2021 15:21:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:21:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:21:31: 1000000 INFO @ Fri, 10 Dec 2021 15:21:36: 2000000 INFO @ Fri, 10 Dec 2021 15:21:41: 3000000 INFO @ Fri, 10 Dec 2021 15:21:47: 4000000 INFO @ Fri, 10 Dec 2021 15:21:52: 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 @ Fri, 10 Dec 2021 15:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.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 @ Fri, 10 Dec 2021 15:21:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:21:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:21:58: 6000000 INFO @ Fri, 10 Dec 2021 15:22:02: 1000000 INFO @ Fri, 10 Dec 2021 15:22:04: 7000000 INFO @ Fri, 10 Dec 2021 15:22:09: 2000000 INFO @ Fri, 10 Dec 2021 15:22:10: 8000000 INFO @ Fri, 10 Dec 2021 15:22:16: 3000000 INFO @ Fri, 10 Dec 2021 15:22:16: 9000000 INFO @ Fri, 10 Dec 2021 15:22:22: 10000000 INFO @ Fri, 10 Dec 2021 15:22:22: 4000000 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 @ Fri, 10 Dec 2021 15:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.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 @ Fri, 10 Dec 2021 15:22:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:22:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:22:28: 11000000 INFO @ Fri, 10 Dec 2021 15:22:29: 5000000 INFO @ Fri, 10 Dec 2021 15:22:32: 1000000 INFO @ Fri, 10 Dec 2021 15:22:34: 12000000 INFO @ Fri, 10 Dec 2021 15:22:36: 6000000 INFO @ Fri, 10 Dec 2021 15:22:39: 2000000 INFO @ Fri, 10 Dec 2021 15:22:41: 13000000 INFO @ Fri, 10 Dec 2021 15:22:42: 7000000 INFO @ Fri, 10 Dec 2021 15:22:46: 3000000 INFO @ Fri, 10 Dec 2021 15:22:47: 14000000 INFO @ Fri, 10 Dec 2021 15:22:49: 8000000 INFO @ Fri, 10 Dec 2021 15:22:53: 4000000 INFO @ Fri, 10 Dec 2021 15:22:53: 15000000 INFO @ Fri, 10 Dec 2021 15:22:56: 9000000 INFO @ Fri, 10 Dec 2021 15:22:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:22:56: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:22:56: #1 total tags in treatment: 15501555 INFO @ Fri, 10 Dec 2021 15:22:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:22:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:22:56: #1 tags after filtering in treatment: 15501555 INFO @ Fri, 10 Dec 2021 15:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:22:56: #1 finished! INFO @ Fri, 10 Dec 2021 15:22:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:22:57: #2 number of paired peaks: 165 WARNING @ Fri, 10 Dec 2021 15:22:57: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 10 Dec 2021 15:22:57: start model_add_line... INFO @ Fri, 10 Dec 2021 15:22:57: start X-correlation... INFO @ Fri, 10 Dec 2021 15:22:57: end of X-cor INFO @ Fri, 10 Dec 2021 15:22:57: #2 finished! INFO @ Fri, 10 Dec 2021 15:22:57: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 15:22:57: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 15:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.05_model.r WARNING @ Fri, 10 Dec 2021 15:22:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:22:57: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 15:22:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:22:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:23:00: 5000000 INFO @ Fri, 10 Dec 2021 15:23:02: 10000000 INFO @ Fri, 10 Dec 2021 15:23:06: 6000000 INFO @ Fri, 10 Dec 2021 15:23:09: 11000000 INFO @ Fri, 10 Dec 2021 15:23:13: 7000000 INFO @ Fri, 10 Dec 2021 15:23:16: 12000000 INFO @ Fri, 10 Dec 2021 15:23:20: 8000000 INFO @ Fri, 10 Dec 2021 15:23:23: 13000000 INFO @ Fri, 10 Dec 2021 15:23:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:23:26: 9000000 INFO @ Fri, 10 Dec 2021 15:23:29: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:23:33: 10000000 INFO @ Fri, 10 Dec 2021 15:23:36: 15000000 INFO @ Fri, 10 Dec 2021 15:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.05_summits.bed INFO @ Fri, 10 Dec 2021 15:23:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4324 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:23:40: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:23:40: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:23:40: #1 total tags in treatment: 15501555 INFO @ Fri, 10 Dec 2021 15:23:40: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:23:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:23:40: 11000000 INFO @ Fri, 10 Dec 2021 15:23:40: #1 tags after filtering in treatment: 15501555 INFO @ Fri, 10 Dec 2021 15:23:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:23:40: #1 finished! INFO @ Fri, 10 Dec 2021 15:23:40: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:23:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:23:41: #2 number of paired peaks: 165 WARNING @ Fri, 10 Dec 2021 15:23:41: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 10 Dec 2021 15:23:41: start model_add_line... INFO @ Fri, 10 Dec 2021 15:23:41: start X-correlation... INFO @ Fri, 10 Dec 2021 15:23:41: end of X-cor INFO @ Fri, 10 Dec 2021 15:23:41: #2 finished! INFO @ Fri, 10 Dec 2021 15:23:41: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 15:23:41: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 15:23:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.10_model.r WARNING @ Fri, 10 Dec 2021 15:23:41: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:23:41: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 15:23:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:23:41: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:23:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:23:46: 12000000 INFO @ Fri, 10 Dec 2021 15:23:52: 13000000 INFO @ Fri, 10 Dec 2021 15:23:59: 14000000 INFO @ Fri, 10 Dec 2021 15:24:05: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:24:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:24:08: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:24:08: #1 total tags in treatment: 15501555 INFO @ Fri, 10 Dec 2021 15:24:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:24:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:24:08: #1 tags after filtering in treatment: 15501555 INFO @ Fri, 10 Dec 2021 15:24:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:24:08: #1 finished! INFO @ Fri, 10 Dec 2021 15:24:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:24:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:24:09: #2 number of paired peaks: 165 WARNING @ Fri, 10 Dec 2021 15:24:09: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Fri, 10 Dec 2021 15:24:09: start model_add_line... INFO @ Fri, 10 Dec 2021 15:24:09: start X-correlation... INFO @ Fri, 10 Dec 2021 15:24:09: end of X-cor INFO @ Fri, 10 Dec 2021 15:24:09: #2 finished! INFO @ Fri, 10 Dec 2021 15:24:09: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 15:24:09: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 15:24:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.20_model.r WARNING @ Fri, 10 Dec 2021 15:24:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:24:09: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 15:24:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:24:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:24:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:24:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.10_summits.bed INFO @ Fri, 10 Dec 2021 15:24:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1639 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:24:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688977/SRX8688977.20_summits.bed INFO @ Fri, 10 Dec 2021 15:24:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (904 records, 4 fields): 3 millis CompletedMACS2peakCalling