Job ID = 16437942 SRX = SRX14148453 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16622084 spots for SRR17992817/SRR17992817.sra Written 16622084 spots for SRR17992817/SRR17992817.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438074 ("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: 00:09:47 16622084 reads; of these: 16622084 (100.00%) were unpaired; of these: 1857664 (11.18%) aligned 0 times 10505912 (63.20%) aligned exactly 1 time 4258508 (25.62%) aligned >1 times 88.82% overall alignment rate Time searching: 00:09:47 Overall time: 00:09:47 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] 1445144 / 14764420 = 0.0979 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 13:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.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 13:31:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:31:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:31:23: 1000000 INFO @ Tue, 02 Aug 2022 13:31:30: 2000000 INFO @ Tue, 02 Aug 2022 13:31:36: 3000000 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 13:31:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.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 13:31:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:31:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:31:43: 4000000 INFO @ Tue, 02 Aug 2022 13:31:51: 5000000 INFO @ Tue, 02 Aug 2022 13:31:51: 1000000 INFO @ Tue, 02 Aug 2022 13:31:59: 6000000 INFO @ Tue, 02 Aug 2022 13:32:01: 2000000 INFO @ Tue, 02 Aug 2022 13:32:07: 7000000 INFO @ Tue, 02 Aug 2022 13:32:09: 3000000 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 13:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.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 13:32:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:32:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:32:15: 8000000 INFO @ Tue, 02 Aug 2022 13:32:17: 4000000 INFO @ Tue, 02 Aug 2022 13:32:21: 1000000 INFO @ Tue, 02 Aug 2022 13:32:23: 9000000 INFO @ Tue, 02 Aug 2022 13:32:26: 5000000 INFO @ Tue, 02 Aug 2022 13:32:29: 2000000 INFO @ Tue, 02 Aug 2022 13:32:31: 10000000 INFO @ Tue, 02 Aug 2022 13:32:34: 6000000 INFO @ Tue, 02 Aug 2022 13:32:38: 3000000 INFO @ Tue, 02 Aug 2022 13:32:40: 11000000 INFO @ Tue, 02 Aug 2022 13:32:42: 7000000 INFO @ Tue, 02 Aug 2022 13:32:47: 4000000 INFO @ Tue, 02 Aug 2022 13:32:48: 12000000 INFO @ Tue, 02 Aug 2022 13:32:50: 8000000 INFO @ Tue, 02 Aug 2022 13:32:54: 5000000 INFO @ Tue, 02 Aug 2022 13:32:56: 13000000 INFO @ Tue, 02 Aug 2022 13:32:58: 9000000 INFO @ Tue, 02 Aug 2022 13:32:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:32:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:32:59: #1 total tags in treatment: 13319276 INFO @ Tue, 02 Aug 2022 13:32:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:32:59: #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 13:32:59: #1 tags after filtering in treatment: 13319276 INFO @ Tue, 02 Aug 2022 13:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:59: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:33:00: #2 number of paired peaks: 645 WARNING @ Tue, 02 Aug 2022 13:33:00: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Tue, 02 Aug 2022 13:33:00: start model_add_line... INFO @ Tue, 02 Aug 2022 13:33:00: start X-correlation... INFO @ Tue, 02 Aug 2022 13:33:00: end of X-cor INFO @ Tue, 02 Aug 2022 13:33:00: #2 finished! INFO @ Tue, 02 Aug 2022 13:33:00: #2 predicted fragment length is 79 bps INFO @ Tue, 02 Aug 2022 13:33:00: #2 alternative fragment length(s) may be 3,79 bps INFO @ Tue, 02 Aug 2022 13:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.05_model.r WARNING @ Tue, 02 Aug 2022 13:33:00: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:33:00: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Tue, 02 Aug 2022 13:33:00: #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 13:33:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:33:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:33:02: 6000000 INFO @ Tue, 02 Aug 2022 13:33:06: 10000000 INFO @ Tue, 02 Aug 2022 13:33:11: 7000000 INFO @ Tue, 02 Aug 2022 13:33:13: 11000000 INFO @ Tue, 02 Aug 2022 13:33:20: 8000000 INFO @ Tue, 02 Aug 2022 13:33:22: 12000000 INFO @ Tue, 02 Aug 2022 13:33:29: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:33:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:33:32: 13000000 INFO @ Tue, 02 Aug 2022 13:33:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:33:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:33:36: #1 total tags in treatment: 13319276 INFO @ Tue, 02 Aug 2022 13:33:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:33:36: #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 13:33:37: #1 tags after filtering in treatment: 13319276 INFO @ Tue, 02 Aug 2022 13:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:33:37: #1 finished! INFO @ Tue, 02 Aug 2022 13:33:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:33:37: 10000000 INFO @ Tue, 02 Aug 2022 13:33:38: #2 number of paired peaks: 645 WARNING @ Tue, 02 Aug 2022 13:33:38: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Tue, 02 Aug 2022 13:33:38: start model_add_line... INFO @ Tue, 02 Aug 2022 13:33:38: start X-correlation... INFO @ Tue, 02 Aug 2022 13:33:38: end of X-cor INFO @ Tue, 02 Aug 2022 13:33:38: #2 finished! INFO @ Tue, 02 Aug 2022 13:33:38: #2 predicted fragment length is 79 bps INFO @ Tue, 02 Aug 2022 13:33:38: #2 alternative fragment length(s) may be 3,79 bps INFO @ Tue, 02 Aug 2022 13:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.10_model.r WARNING @ Tue, 02 Aug 2022 13:33:38: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:33:38: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Tue, 02 Aug 2022 13:33:38: #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 13:33:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:33:45: 11000000 INFO @ Tue, 02 Aug 2022 13:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.05_summits.bed INFO @ Tue, 02 Aug 2022 13:33:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2189 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:33:52: 12000000 INFO @ Tue, 02 Aug 2022 13:33:58: 13000000 INFO @ Tue, 02 Aug 2022 13:34:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:34:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:34:01: #1 total tags in treatment: 13319276 INFO @ Tue, 02 Aug 2022 13:34:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:34:01: #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 13:34:01: #1 tags after filtering in treatment: 13319276 INFO @ Tue, 02 Aug 2022 13:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:34:01: #1 finished! INFO @ Tue, 02 Aug 2022 13:34:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:34:02: #2 number of paired peaks: 645 WARNING @ Tue, 02 Aug 2022 13:34:02: Fewer paired peaks (645) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 645 pairs to build model! INFO @ Tue, 02 Aug 2022 13:34:02: start model_add_line... INFO @ Tue, 02 Aug 2022 13:34:02: start X-correlation... INFO @ Tue, 02 Aug 2022 13:34:02: end of X-cor INFO @ Tue, 02 Aug 2022 13:34:02: #2 finished! INFO @ Tue, 02 Aug 2022 13:34:02: #2 predicted fragment length is 79 bps INFO @ Tue, 02 Aug 2022 13:34:02: #2 alternative fragment length(s) may be 3,79 bps INFO @ Tue, 02 Aug 2022 13:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.20_model.r WARNING @ Tue, 02 Aug 2022 13:34:02: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:34:02: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Tue, 02 Aug 2022 13:34:02: #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 13:34:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:34:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:34:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:34:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:34:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:34:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.10_summits.bed INFO @ Tue, 02 Aug 2022 13:34:22: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1268 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:34:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:34:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:34:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:34:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148453/SRX14148453.20_summits.bed INFO @ Tue, 02 Aug 2022 13:34:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (644 records, 4 fields): 32 millis CompletedMACS2peakCalling