Job ID = 16432276 SRX = SRX15407775 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:31:55 prefetch.2.10.7: 1) Downloading 'SRR19348979'... 2022-08-02T00:31:55 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:32:22 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:32:22 prefetch.2.10.7: 'SRR19348979' is valid 2022-08-02T00:32:22 prefetch.2.10.7: 1) 'SRR19348979' was downloaded successfully 2022-08-02T00:32:22 prefetch.2.10.7: 'SRR19348979' has 0 unresolved dependencies Read 11737620 spots for SRR19348979/SRR19348979.sra Written 11737620 spots for SRR19348979/SRR19348979.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433316 ("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: 00:03:26 11737620 reads; of these: 11737620 (100.00%) were unpaired; of these: 1452042 (12.37%) aligned 0 times 8797257 (74.95%) aligned exactly 1 time 1488321 (12.68%) aligned >1 times 87.63% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1625164 / 10285578 = 0.1580 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 09:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.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 09:39:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:39:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:39:13: 1000000 INFO @ Tue, 02 Aug 2022 09:39:19: 2000000 INFO @ Tue, 02 Aug 2022 09:39:25: 3000000 INFO @ Tue, 02 Aug 2022 09:39:30: 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 09:39:36: 5000000 INFO @ Tue, 02 Aug 2022 09:39:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.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 09:39:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:39:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:39:42: 6000000 INFO @ Tue, 02 Aug 2022 09:39:43: 1000000 INFO @ Tue, 02 Aug 2022 09:39:48: 7000000 INFO @ Tue, 02 Aug 2022 09:39:49: 2000000 INFO @ Tue, 02 Aug 2022 09:39:54: 8000000 INFO @ Tue, 02 Aug 2022 09:39:55: 3000000 INFO @ Tue, 02 Aug 2022 09:39:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:39:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:39:58: #1 total tags in treatment: 8660414 INFO @ Tue, 02 Aug 2022 09:39:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:39:58: #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 09:39:58: #1 tags after filtering in treatment: 8660414 INFO @ Tue, 02 Aug 2022 09:39:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:39:58: #1 finished! INFO @ Tue, 02 Aug 2022 09:39:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:39:58: #2 number of paired peaks: 304 WARNING @ Tue, 02 Aug 2022 09:39:58: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 02 Aug 2022 09:39:58: start model_add_line... INFO @ Tue, 02 Aug 2022 09:39:58: start X-correlation... INFO @ Tue, 02 Aug 2022 09:39:58: end of X-cor INFO @ Tue, 02 Aug 2022 09:39:58: #2 finished! INFO @ Tue, 02 Aug 2022 09:39:58: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 09:39:58: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 09:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.05_model.r WARNING @ Tue, 02 Aug 2022 09:39:58: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:39:58: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 09:39:58: #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 09:39:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:40:01: 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 09:40:07: 5000000 INFO @ Tue, 02 Aug 2022 09:40:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.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 09:40:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:40:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:40:12: 6000000 INFO @ Tue, 02 Aug 2022 09:40:12: 1000000 INFO @ Tue, 02 Aug 2022 09:40:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:40:18: 7000000 INFO @ Tue, 02 Aug 2022 09:40:18: 2000000 INFO @ Tue, 02 Aug 2022 09:40:24: 8000000 INFO @ Tue, 02 Aug 2022 09:40:24: 3000000 INFO @ Tue, 02 Aug 2022 09:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.05_summits.bed INFO @ Tue, 02 Aug 2022 09:40:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1952 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:40:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:40:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:40:27: #1 total tags in treatment: 8660414 INFO @ Tue, 02 Aug 2022 09:40:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:40:27: #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 09:40:28: #1 tags after filtering in treatment: 8660414 INFO @ Tue, 02 Aug 2022 09:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:40:28: #1 finished! INFO @ Tue, 02 Aug 2022 09:40:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:40:28: #2 number of paired peaks: 304 WARNING @ Tue, 02 Aug 2022 09:40:28: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 02 Aug 2022 09:40:28: start model_add_line... INFO @ Tue, 02 Aug 2022 09:40:28: start X-correlation... INFO @ Tue, 02 Aug 2022 09:40:28: end of X-cor INFO @ Tue, 02 Aug 2022 09:40:28: #2 finished! INFO @ Tue, 02 Aug 2022 09:40:28: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 09:40:28: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 09:40:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.10_model.r WARNING @ Tue, 02 Aug 2022 09:40:28: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:40:28: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 09:40:28: #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 09:40:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:40:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:40:30: 4000000 INFO @ Tue, 02 Aug 2022 09:40:35: 5000000 INFO @ Tue, 02 Aug 2022 09:40:41: 6000000 INFO @ Tue, 02 Aug 2022 09:40:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:40:46: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:40:52: 8000000 INFO @ Tue, 02 Aug 2022 09:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.10_summits.bed INFO @ Tue, 02 Aug 2022 09:40:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (794 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:40:56: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:40:56: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:40:56: #1 total tags in treatment: 8660414 INFO @ Tue, 02 Aug 2022 09:40:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:40:56: #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 09:40:56: #1 tags after filtering in treatment: 8660414 INFO @ Tue, 02 Aug 2022 09:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:40:56: #1 finished! INFO @ Tue, 02 Aug 2022 09:40:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:40:56: #2 number of paired peaks: 304 WARNING @ Tue, 02 Aug 2022 09:40:56: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 02 Aug 2022 09:40:56: start model_add_line... INFO @ Tue, 02 Aug 2022 09:40:56: start X-correlation... INFO @ Tue, 02 Aug 2022 09:40:57: end of X-cor INFO @ Tue, 02 Aug 2022 09:40:57: #2 finished! INFO @ Tue, 02 Aug 2022 09:40:57: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 09:40:57: #2 alternative fragment length(s) may be 4,76 bps INFO @ Tue, 02 Aug 2022 09:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.20_model.r WARNING @ Tue, 02 Aug 2022 09:40:57: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 09:40:57: #2 You may need to consider one of the other alternative d(s): 4,76 WARNING @ Tue, 02 Aug 2022 09:40:57: #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 09:40:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:40:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:41:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407775/SRX15407775.20_summits.bed INFO @ Tue, 02 Aug 2022 09:41:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (238 records, 4 fields): 18 millis CompletedMACS2peakCalling