Job ID = 16438049 SRX = SRX12261349 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21879036 spots for SRR15972605/SRR15972605.sra Written 21879036 spots for SRR15972605/SRR15972605.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438144 ("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: 00:16:36 21879036 reads; of these: 21879036 (100.00%) were unpaired; of these: 680777 (3.11%) aligned 0 times 12579092 (57.49%) aligned exactly 1 time 8619167 (39.39%) aligned >1 times 96.89% overall alignment rate Time searching: 00:16:36 Overall time: 00:16:36 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] 9567755 / 21198259 = 0.4513 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.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 @ Tue, 02 Aug 2022 13:47:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:47:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:48:03: 1000000 INFO @ Tue, 02 Aug 2022 13:48:13: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:48:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.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 @ Tue, 02 Aug 2022 13:48:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:48:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:48:22: 3000000 INFO @ Tue, 02 Aug 2022 13:48:32: 1000000 INFO @ Tue, 02 Aug 2022 13:48:33: 4000000 INFO @ Tue, 02 Aug 2022 13:48:43: 2000000 INFO @ Tue, 02 Aug 2022 13:48:43: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:48:53: 3000000 INFO @ Tue, 02 Aug 2022 13:48:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.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 @ Tue, 02 Aug 2022 13:48:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:48:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:48:54: 6000000 INFO @ Tue, 02 Aug 2022 13:49:03: 4000000 INFO @ Tue, 02 Aug 2022 13:49:04: 1000000 INFO @ Tue, 02 Aug 2022 13:49:04: 7000000 INFO @ Tue, 02 Aug 2022 13:49:13: 5000000 INFO @ Tue, 02 Aug 2022 13:49:15: 2000000 INFO @ Tue, 02 Aug 2022 13:49:15: 8000000 INFO @ Tue, 02 Aug 2022 13:49:22: 6000000 INFO @ Tue, 02 Aug 2022 13:49:25: 9000000 INFO @ Tue, 02 Aug 2022 13:49:26: 3000000 INFO @ Tue, 02 Aug 2022 13:49:32: 7000000 INFO @ Tue, 02 Aug 2022 13:49:36: 10000000 INFO @ Tue, 02 Aug 2022 13:49:36: 4000000 INFO @ Tue, 02 Aug 2022 13:49:42: 8000000 INFO @ Tue, 02 Aug 2022 13:49:47: 11000000 INFO @ Tue, 02 Aug 2022 13:49:47: 5000000 INFO @ Tue, 02 Aug 2022 13:49:51: 9000000 INFO @ Tue, 02 Aug 2022 13:49:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:49:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:49:53: #1 total tags in treatment: 11630504 INFO @ Tue, 02 Aug 2022 13:49:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:49:53: #1 tags after filtering in treatment: 11630504 INFO @ Tue, 02 Aug 2022 13:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:49:53: #1 finished! INFO @ Tue, 02 Aug 2022 13:49:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:49:54: #2 number of paired peaks: 300 WARNING @ Tue, 02 Aug 2022 13:49:54: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 02 Aug 2022 13:49:54: start model_add_line... INFO @ Tue, 02 Aug 2022 13:49:54: start X-correlation... INFO @ Tue, 02 Aug 2022 13:49:54: end of X-cor INFO @ Tue, 02 Aug 2022 13:49:54: #2 finished! INFO @ Tue, 02 Aug 2022 13:49:54: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:49:54: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.05_model.r WARNING @ Tue, 02 Aug 2022 13:49:55: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:49:55: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:49:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:49:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:49:58: 6000000 INFO @ Tue, 02 Aug 2022 13:50:00: 10000000 INFO @ Tue, 02 Aug 2022 13:50:09: 7000000 INFO @ Tue, 02 Aug 2022 13:50:09: 11000000 INFO @ Tue, 02 Aug 2022 13:50:15: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:50:15: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:50:15: #1 total tags in treatment: 11630504 INFO @ Tue, 02 Aug 2022 13:50:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:50:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:50:15: #1 tags after filtering in treatment: 11630504 INFO @ Tue, 02 Aug 2022 13:50:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:50:15: #1 finished! INFO @ Tue, 02 Aug 2022 13:50:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:50:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:50:16: #2 number of paired peaks: 300 WARNING @ Tue, 02 Aug 2022 13:50:16: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 02 Aug 2022 13:50:16: start model_add_line... INFO @ Tue, 02 Aug 2022 13:50:16: start X-correlation... INFO @ Tue, 02 Aug 2022 13:50:16: end of X-cor INFO @ Tue, 02 Aug 2022 13:50:16: #2 finished! INFO @ Tue, 02 Aug 2022 13:50:16: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:50:16: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:50:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.10_model.r WARNING @ Tue, 02 Aug 2022 13:50:16: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:50:16: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:50:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:50:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:50:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:50:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:50:20: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:50:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:50:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:50:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.05_summits.bed INFO @ Tue, 02 Aug 2022 13:50:30: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6003 records, 4 fields): 82 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:50:31: 9000000 INFO @ Tue, 02 Aug 2022 13:50:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:50:41: 10000000 INFO @ Tue, 02 Aug 2022 13:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.10_summits.bed INFO @ Tue, 02 Aug 2022 13:50:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3104 records, 4 fields): 97 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:50:52: 11000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:50:59: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:50:59: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:50:59: #1 total tags in treatment: 11630504 INFO @ Tue, 02 Aug 2022 13:50:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:50:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:50:59: #1 tags after filtering in treatment: 11630504 INFO @ Tue, 02 Aug 2022 13:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:50:59: #1 finished! INFO @ Tue, 02 Aug 2022 13:50:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:51:00: #2 number of paired peaks: 300 WARNING @ Tue, 02 Aug 2022 13:51:00: Fewer paired peaks (300) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 300 pairs to build model! INFO @ Tue, 02 Aug 2022 13:51:00: start model_add_line... INFO @ Tue, 02 Aug 2022 13:51:00: start X-correlation... INFO @ Tue, 02 Aug 2022 13:51:00: end of X-cor INFO @ Tue, 02 Aug 2022 13:51:00: #2 finished! INFO @ Tue, 02 Aug 2022 13:51:00: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 13:51:00: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 13:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.20_model.r WARNING @ Tue, 02 Aug 2022 13:51:00: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:51:00: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 13:51:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:51:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:51:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261349/SRX12261349.20_summits.bed INFO @ Tue, 02 Aug 2022 13:51:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (996 records, 4 fields): 21 millis CompletedMACS2peakCalling