Job ID = 16432464 SRX = SRX15407789 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:32:23 prefetch.2.10.7: 1) Downloading 'SRR19348962'... 2022-08-02T00:32:24 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:03 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:04 prefetch.2.10.7: 'SRR19348962' is valid 2022-08-02T00:33:04 prefetch.2.10.7: 1) 'SRR19348962' was downloaded successfully 2022-08-02T00:33:04 prefetch.2.10.7: 'SRR19348962' has 0 unresolved dependencies Read 18509223 spots for SRR19348962/SRR19348962.sra Written 18509223 spots for SRR19348962/SRR19348962.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433759 ("srTce11") 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: 00:06:04 18509223 reads; of these: 18509223 (100.00%) were unpaired; of these: 526624 (2.85%) aligned 0 times 15358700 (82.98%) aligned exactly 1 time 2623899 (14.18%) aligned >1 times 97.15% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1888228 / 17982599 = 0.1050 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 09:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.bam'] # control file = None # effective genome size = 9.00e+07 # 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 09:46:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:46:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:46:43: 1000000 INFO @ Tue, 02 Aug 2022 09:46:50: 2000000 INFO @ Tue, 02 Aug 2022 09:46:57: 3000000 INFO @ Tue, 02 Aug 2022 09:47:03: 4000000 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 09:47:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.bam'] # control file = None # effective genome size = 9.00e+07 # 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 09:47:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:10: 5000000 INFO @ Tue, 02 Aug 2022 09:47:13: 1000000 INFO @ Tue, 02 Aug 2022 09:47:17: 6000000 INFO @ Tue, 02 Aug 2022 09:47:20: 2000000 INFO @ Tue, 02 Aug 2022 09:47:25: 7000000 INFO @ Tue, 02 Aug 2022 09:47:27: 3000000 INFO @ Tue, 02 Aug 2022 09:47:31: 8000000 INFO @ Tue, 02 Aug 2022 09:47:33: 4000000 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 09:47:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.bam'] # control file = None # effective genome size = 9.00e+07 # 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 09:47:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:47:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:47:39: 9000000 INFO @ Tue, 02 Aug 2022 09:47:41: 5000000 INFO @ Tue, 02 Aug 2022 09:47:44: 1000000 INFO @ Tue, 02 Aug 2022 09:47:46: 10000000 INFO @ Tue, 02 Aug 2022 09:47:48: 6000000 INFO @ Tue, 02 Aug 2022 09:47:51: 2000000 INFO @ Tue, 02 Aug 2022 09:47:54: 11000000 INFO @ Tue, 02 Aug 2022 09:47:54: 7000000 INFO @ Tue, 02 Aug 2022 09:47:59: 3000000 INFO @ Tue, 02 Aug 2022 09:48:01: 8000000 INFO @ Tue, 02 Aug 2022 09:48:02: 12000000 INFO @ Tue, 02 Aug 2022 09:48:06: 4000000 INFO @ Tue, 02 Aug 2022 09:48:08: 9000000 INFO @ Tue, 02 Aug 2022 09:48:09: 13000000 INFO @ Tue, 02 Aug 2022 09:48:13: 5000000 INFO @ Tue, 02 Aug 2022 09:48:15: 10000000 INFO @ Tue, 02 Aug 2022 09:48:17: 14000000 INFO @ Tue, 02 Aug 2022 09:48:20: 6000000 INFO @ Tue, 02 Aug 2022 09:48:22: 11000000 INFO @ Tue, 02 Aug 2022 09:48:24: 15000000 INFO @ Tue, 02 Aug 2022 09:48:28: 7000000 INFO @ Tue, 02 Aug 2022 09:48:29: 12000000 INFO @ Tue, 02 Aug 2022 09:48:32: 16000000 INFO @ Tue, 02 Aug 2022 09:48:33: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:48:33: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:48:33: #1 total tags in treatment: 16094371 INFO @ Tue, 02 Aug 2022 09:48:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:48:33: #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 09:48:33: #1 tags after filtering in treatment: 16094371 INFO @ Tue, 02 Aug 2022 09:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:48:33: #1 finished! INFO @ Tue, 02 Aug 2022 09:48:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:48:34: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:48:34: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:48:34: start model_add_line... INFO @ Tue, 02 Aug 2022 09:48:34: start X-correlation... INFO @ Tue, 02 Aug 2022 09:48:34: end of X-cor INFO @ Tue, 02 Aug 2022 09:48:34: #2 finished! INFO @ Tue, 02 Aug 2022 09:48:34: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 09:48:34: #2 alternative fragment length(s) may be 2,77 bps INFO @ Tue, 02 Aug 2022 09:48:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.05_model.r WARNING @ Tue, 02 Aug 2022 09:48:34: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:48:34: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Tue, 02 Aug 2022 09:48:34: #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 09:48:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:48:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:48:35: 8000000 INFO @ Tue, 02 Aug 2022 09:48:36: 13000000 INFO @ Tue, 02 Aug 2022 09:48:42: 9000000 INFO @ Tue, 02 Aug 2022 09:48:43: 14000000 INFO @ Tue, 02 Aug 2022 09:48:49: 10000000 INFO @ Tue, 02 Aug 2022 09:48:50: 15000000 INFO @ Tue, 02 Aug 2022 09:48:56: 11000000 INFO @ Tue, 02 Aug 2022 09:48:57: 16000000 INFO @ Tue, 02 Aug 2022 09:48:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:48:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:48:58: #1 total tags in treatment: 16094371 INFO @ Tue, 02 Aug 2022 09:48:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:48:58: #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 09:48:58: #1 tags after filtering in treatment: 16094371 INFO @ Tue, 02 Aug 2022 09:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:48:58: #1 finished! INFO @ Tue, 02 Aug 2022 09:48:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:48:59: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:48:59: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:48:59: start model_add_line... INFO @ Tue, 02 Aug 2022 09:48:59: start X-correlation... INFO @ Tue, 02 Aug 2022 09:48:59: end of X-cor INFO @ Tue, 02 Aug 2022 09:48:59: #2 finished! INFO @ Tue, 02 Aug 2022 09:48:59: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 09:48:59: #2 alternative fragment length(s) may be 2,77 bps INFO @ Tue, 02 Aug 2022 09:48:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.10_model.r WARNING @ Tue, 02 Aug 2022 09:48:59: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:48:59: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Tue, 02 Aug 2022 09:48:59: #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 09:48:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:49:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:49:03: 12000000 INFO @ Tue, 02 Aug 2022 09:49:10: 13000000 INFO @ Tue, 02 Aug 2022 09:49:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:49:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:49:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.05_summits.bed INFO @ Tue, 02 Aug 2022 09:49:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:49:17: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:49:24: 15000000 INFO @ Tue, 02 Aug 2022 09:49:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:49:30: 16000000 INFO @ Tue, 02 Aug 2022 09:49:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:49:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:49:31: #1 total tags in treatment: 16094371 INFO @ Tue, 02 Aug 2022 09:49:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:49:31: #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 09:49:31: #1 tags after filtering in treatment: 16094371 INFO @ Tue, 02 Aug 2022 09:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:49:31: #1 finished! INFO @ Tue, 02 Aug 2022 09:49:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:49:32: #2 number of paired peaks: 184 WARNING @ Tue, 02 Aug 2022 09:49:32: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 02 Aug 2022 09:49:32: start model_add_line... INFO @ Tue, 02 Aug 2022 09:49:33: start X-correlation... INFO @ Tue, 02 Aug 2022 09:49:33: end of X-cor INFO @ Tue, 02 Aug 2022 09:49:33: #2 finished! INFO @ Tue, 02 Aug 2022 09:49:33: #2 predicted fragment length is 77 bps INFO @ Tue, 02 Aug 2022 09:49:33: #2 alternative fragment length(s) may be 2,77 bps INFO @ Tue, 02 Aug 2022 09:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.20_model.r WARNING @ Tue, 02 Aug 2022 09:49:33: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:49:33: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Tue, 02 Aug 2022 09:49:33: #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 09:49:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:49:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:49:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:49:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.10_summits.bed INFO @ Tue, 02 Aug 2022 09:49:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (372 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:49:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407789/SRX15407789.20_summits.bed INFO @ Tue, 02 Aug 2022 09:50:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。