Job ID = 16436186 SRX = SRX15369012 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:02:23 prefetch.2.10.7: 1) Downloading 'SRR19308741'... 2022-08-02T02:02:23 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:03:09 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:03:09 prefetch.2.10.7: 1) 'SRR19308741' was downloaded successfully 2022-08-02T02:03:09 prefetch.2.10.7: 'SRR19308741' has 0 unresolved dependencies Read 21030331 spots for SRR19308741/SRR19308741.sra Written 21030331 spots for SRR19308741/SRR19308741.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436367 ("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: 00:12:38 21030331 reads; of these: 21030331 (100.00%) were unpaired; of these: 623694 (2.97%) aligned 0 times 12337321 (58.66%) aligned exactly 1 time 8069316 (38.37%) aligned >1 times 97.03% overall alignment rate Time searching: 00:12:38 Overall time: 00:12:38 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] 9901486 / 20406637 = 0.4852 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 11:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.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 11:21:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:21:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:21:51: 1000000 INFO @ Tue, 02 Aug 2022 11:21:58: 2000000 INFO @ Tue, 02 Aug 2022 11:22:05: 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 11:22:12: 4000000 INFO @ Tue, 02 Aug 2022 11:22:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.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 11:22:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:22:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:22:19: 5000000 INFO @ Tue, 02 Aug 2022 11:22:21: 1000000 INFO @ Tue, 02 Aug 2022 11:22:27: 6000000 INFO @ Tue, 02 Aug 2022 11:22:28: 2000000 INFO @ Tue, 02 Aug 2022 11:22:34: 7000000 INFO @ Tue, 02 Aug 2022 11:22:36: 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 11:22:42: 8000000 INFO @ Tue, 02 Aug 2022 11:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.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 11:22:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:22:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:22:44: 4000000 INFO @ Tue, 02 Aug 2022 11:22:49: 9000000 INFO @ Tue, 02 Aug 2022 11:22:51: 5000000 INFO @ Tue, 02 Aug 2022 11:22:51: 1000000 INFO @ Tue, 02 Aug 2022 11:22:57: 10000000 INFO @ Tue, 02 Aug 2022 11:22:58: 6000000 INFO @ Tue, 02 Aug 2022 11:22:58: 2000000 INFO @ Tue, 02 Aug 2022 11:23:01: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:23:01: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:23:01: #1 total tags in treatment: 10505151 INFO @ Tue, 02 Aug 2022 11:23:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:23:01: #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 11:23:01: #1 tags after filtering in treatment: 10505151 INFO @ Tue, 02 Aug 2022 11:23:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:23:01: #1 finished! INFO @ Tue, 02 Aug 2022 11:23:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:23:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:23:01: #2 number of paired peaks: 321 WARNING @ Tue, 02 Aug 2022 11:23:01: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 02 Aug 2022 11:23:01: start model_add_line... INFO @ Tue, 02 Aug 2022 11:23:02: start X-correlation... INFO @ Tue, 02 Aug 2022 11:23:02: end of X-cor INFO @ Tue, 02 Aug 2022 11:23:02: #2 finished! INFO @ Tue, 02 Aug 2022 11:23:02: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:23:02: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 11:23:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.05_model.r WARNING @ Tue, 02 Aug 2022 11:23:02: #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 11:23:02: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 11:23:02: #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 11:23:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:23:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:23:05: 7000000 INFO @ Tue, 02 Aug 2022 11:23:06: 3000000 INFO @ Tue, 02 Aug 2022 11:23:12: 8000000 INFO @ Tue, 02 Aug 2022 11:23:13: 4000000 INFO @ Tue, 02 Aug 2022 11:23:19: 9000000 INFO @ Tue, 02 Aug 2022 11:23:21: 5000000 INFO @ Tue, 02 Aug 2022 11:23:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:23:27: 10000000 INFO @ Tue, 02 Aug 2022 11:23:29: 6000000 INFO @ Tue, 02 Aug 2022 11:23:31: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:23:31: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:23:31: #1 total tags in treatment: 10505151 INFO @ Tue, 02 Aug 2022 11:23:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:23:31: #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 11:23:31: #1 tags after filtering in treatment: 10505151 INFO @ Tue, 02 Aug 2022 11:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:23:31: #1 finished! INFO @ Tue, 02 Aug 2022 11:23:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:23:32: #2 number of paired peaks: 321 WARNING @ Tue, 02 Aug 2022 11:23:32: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 02 Aug 2022 11:23:32: start model_add_line... INFO @ Tue, 02 Aug 2022 11:23:32: start X-correlation... INFO @ Tue, 02 Aug 2022 11:23:32: end of X-cor INFO @ Tue, 02 Aug 2022 11:23:32: #2 finished! INFO @ Tue, 02 Aug 2022 11:23:32: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:23:32: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 11:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.10_model.r WARNING @ Tue, 02 Aug 2022 11:23:32: #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 11:23:32: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 11:23:32: #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 11:23:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.05_summits.bed INFO @ Tue, 02 Aug 2022 11:23:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5956 records, 4 fields): 47 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:23:35: 7000000 INFO @ Tue, 02 Aug 2022 11:23:42: 8000000 INFO @ Tue, 02 Aug 2022 11:23:49: 9000000 INFO @ Tue, 02 Aug 2022 11:23:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:23:55: 10000000 INFO @ Tue, 02 Aug 2022 11:23:59: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:23:59: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:23:59: #1 total tags in treatment: 10505151 INFO @ Tue, 02 Aug 2022 11:23:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:23:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:23:59: #1 tags after filtering in treatment: 10505151 INFO @ Tue, 02 Aug 2022 11:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:23:59: #1 finished! INFO @ Tue, 02 Aug 2022 11:23:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:24:00: #2 number of paired peaks: 321 WARNING @ Tue, 02 Aug 2022 11:24:00: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 02 Aug 2022 11:24:00: start model_add_line... INFO @ Tue, 02 Aug 2022 11:24:00: start X-correlation... INFO @ Tue, 02 Aug 2022 11:24:00: end of X-cor INFO @ Tue, 02 Aug 2022 11:24:00: #2 finished! INFO @ Tue, 02 Aug 2022 11:24:00: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:24:00: #2 alternative fragment length(s) may be 72 bps INFO @ Tue, 02 Aug 2022 11:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.20_model.r WARNING @ Tue, 02 Aug 2022 11:24:00: #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 11:24:00: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Tue, 02 Aug 2022 11:24:00: #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 11:24:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.10_summits.bed INFO @ Tue, 02 Aug 2022 11:24:04: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2831 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:24:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:24:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:24:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:24:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369012/SRX15369012.20_summits.bed INFO @ Tue, 02 Aug 2022 11:24:32: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (838 records, 4 fields): 14 millis CompletedMACS2peakCalling