Job ID = 16432339 SRX = SRX15407780 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:32:11 prefetch.2.10.7: 1) Downloading 'SRR19348971'... 2022-08-02T00:32:11 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:32:55 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:32:56 prefetch.2.10.7: 'SRR19348971' is valid 2022-08-02T00:32:56 prefetch.2.10.7: 1) 'SRR19348971' was downloaded successfully 2022-08-02T00:32:56 prefetch.2.10.7: 'SRR19348971' has 0 unresolved dependencies Read 16524259 spots for SRR19348971/SRR19348971.sra Written 16524259 spots for SRR19348971/SRR19348971.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433628 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:21 16524259 reads; of these: 16524259 (100.00%) were unpaired; of these: 1988769 (12.04%) aligned 0 times 12589109 (76.19%) aligned exactly 1 time 1946381 (11.78%) aligned >1 times 87.96% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 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] 2004594 / 14535490 = 0.1379 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 09:43:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.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 09:43:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:43:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:43:20: 1000000 INFO @ Tue, 02 Aug 2022 09:43:26: 2000000 INFO @ Tue, 02 Aug 2022 09:43:31: 3000000 INFO @ Tue, 02 Aug 2022 09:43:37: 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 09:43:42: 5000000 INFO @ Tue, 02 Aug 2022 09:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.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 09:43:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:43:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:43:49: 6000000 INFO @ Tue, 02 Aug 2022 09:43:50: 1000000 INFO @ Tue, 02 Aug 2022 09:43:55: 7000000 INFO @ Tue, 02 Aug 2022 09:43:57: 2000000 INFO @ Tue, 02 Aug 2022 09:44:01: 8000000 INFO @ Tue, 02 Aug 2022 09:44:03: 3000000 INFO @ Tue, 02 Aug 2022 09:44:08: 9000000 INFO @ Tue, 02 Aug 2022 09:44:09: 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 09:44:14: 10000000 INFO @ Tue, 02 Aug 2022 09:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.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 09:44:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:44:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:44:15: 5000000 INFO @ Tue, 02 Aug 2022 09:44:20: 11000000 INFO @ Tue, 02 Aug 2022 09:44:21: 1000000 INFO @ Tue, 02 Aug 2022 09:44:22: 6000000 INFO @ Tue, 02 Aug 2022 09:44:27: 12000000 INFO @ Tue, 02 Aug 2022 09:44:28: 2000000 INFO @ Tue, 02 Aug 2022 09:44:28: 7000000 INFO @ Tue, 02 Aug 2022 09:44:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:44:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:44:30: #1 total tags in treatment: 12530896 INFO @ Tue, 02 Aug 2022 09:44:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:44:30: #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 09:44:30: #1 tags after filtering in treatment: 12530896 INFO @ Tue, 02 Aug 2022 09:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:44:30: #1 finished! INFO @ Tue, 02 Aug 2022 09:44:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:44:31: #2 number of paired peaks: 486 WARNING @ Tue, 02 Aug 2022 09:44:31: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 02 Aug 2022 09:44:31: start model_add_line... INFO @ Tue, 02 Aug 2022 09:44:31: start X-correlation... INFO @ Tue, 02 Aug 2022 09:44:31: end of X-cor INFO @ Tue, 02 Aug 2022 09:44:31: #2 finished! INFO @ Tue, 02 Aug 2022 09:44:31: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 09:44:31: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 09:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.05_model.r INFO @ Tue, 02 Aug 2022 09:44:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:44:35: 8000000 INFO @ Tue, 02 Aug 2022 09:44:36: 3000000 INFO @ Tue, 02 Aug 2022 09:44:41: 9000000 INFO @ Tue, 02 Aug 2022 09:44:43: 4000000 INFO @ Tue, 02 Aug 2022 09:44:48: 10000000 INFO @ Tue, 02 Aug 2022 09:44:51: 5000000 INFO @ Tue, 02 Aug 2022 09:44:54: 11000000 INFO @ Tue, 02 Aug 2022 09:44:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:44:58: 6000000 INFO @ Tue, 02 Aug 2022 09:45:01: 12000000 INFO @ Tue, 02 Aug 2022 09:45:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:45:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:45:04: #1 total tags in treatment: 12530896 INFO @ Tue, 02 Aug 2022 09:45:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:45:04: #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 09:45:04: #1 tags after filtering in treatment: 12530896 INFO @ Tue, 02 Aug 2022 09:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:45:04: #1 finished! INFO @ Tue, 02 Aug 2022 09:45:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:45:05: 7000000 INFO @ Tue, 02 Aug 2022 09:45:05: #2 number of paired peaks: 486 WARNING @ Tue, 02 Aug 2022 09:45:05: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 02 Aug 2022 09:45:05: start model_add_line... INFO @ Tue, 02 Aug 2022 09:45:05: start X-correlation... INFO @ Tue, 02 Aug 2022 09:45:05: end of X-cor INFO @ Tue, 02 Aug 2022 09:45:05: #2 finished! INFO @ Tue, 02 Aug 2022 09:45:05: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 09:45:05: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 09:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.10_model.r INFO @ Tue, 02 Aug 2022 09:45:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:45:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.05_summits.bed INFO @ Tue, 02 Aug 2022 09:45:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6308 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:45:12: 8000000 INFO @ Tue, 02 Aug 2022 09:45:18: 9000000 INFO @ Tue, 02 Aug 2022 09:45:24: 10000000 INFO @ Tue, 02 Aug 2022 09:45:30: 11000000 INFO @ Tue, 02 Aug 2022 09:45:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:45:36: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:45:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:45:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:45:39: #1 total tags in treatment: 12530896 INFO @ Tue, 02 Aug 2022 09:45:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:45:39: #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 09:45:39: #1 tags after filtering in treatment: 12530896 INFO @ Tue, 02 Aug 2022 09:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:45:39: #1 finished! INFO @ Tue, 02 Aug 2022 09:45:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:45:40: #2 number of paired peaks: 486 WARNING @ Tue, 02 Aug 2022 09:45:40: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Tue, 02 Aug 2022 09:45:40: start model_add_line... INFO @ Tue, 02 Aug 2022 09:45:40: start X-correlation... INFO @ Tue, 02 Aug 2022 09:45:40: end of X-cor INFO @ Tue, 02 Aug 2022 09:45:40: #2 finished! INFO @ Tue, 02 Aug 2022 09:45:40: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 09:45:40: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 09:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.20_model.r INFO @ Tue, 02 Aug 2022 09:45:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:45:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:45:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:45:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.10_summits.bed INFO @ Tue, 02 Aug 2022 09:45:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4120 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:46:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407780/SRX15407780.20_summits.bed INFO @ Tue, 02 Aug 2022 09:46:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2288 records, 4 fields): 29 millis CompletedMACS2peakCalling