Job ID = 16435593 SRX = SRX13110375 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:52:01 prefetch.2.10.7: 1) Downloading 'SRR16918045'... 2022-08-02T01:52:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:52:27 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:52:28 prefetch.2.10.7: 'SRR16918045' is valid 2022-08-02T01:52:28 prefetch.2.10.7: 1) 'SRR16918045' was downloaded successfully 2022-08-02T01:52:28 prefetch.2.10.7: 'SRR16918045' has 0 unresolved dependencies Read 14042144 spots for SRR16918045/SRR16918045.sra Written 14042144 spots for SRR16918045/SRR16918045.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436161 ("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: 00:04:11 14042144 reads; of these: 14042144 (100.00%) were unpaired; of these: 1435132 (10.22%) aligned 0 times 10821240 (77.06%) aligned exactly 1 time 1785772 (12.72%) aligned >1 times 89.78% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 2177821 / 12607012 = 0.1727 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 11:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.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 11:00:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:37: 1000000 INFO @ Tue, 02 Aug 2022 11:00:43: 2000000 INFO @ Tue, 02 Aug 2022 11:00:49: 3000000 INFO @ Tue, 02 Aug 2022 11:00:55: 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 11:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.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 11:01:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:02: 5000000 INFO @ Tue, 02 Aug 2022 11:01:08: 1000000 INFO @ Tue, 02 Aug 2022 11:01:10: 6000000 INFO @ Tue, 02 Aug 2022 11:01:15: 2000000 INFO @ Tue, 02 Aug 2022 11:01:17: 7000000 INFO @ Tue, 02 Aug 2022 11:01:22: 3000000 INFO @ Tue, 02 Aug 2022 11:01:24: 8000000 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 11:01:30: 4000000 INFO @ Tue, 02 Aug 2022 11:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.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 11:01:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:32: 9000000 INFO @ Tue, 02 Aug 2022 11:01:38: 5000000 INFO @ Tue, 02 Aug 2022 11:01:38: 1000000 INFO @ Tue, 02 Aug 2022 11:01:40: 10000000 INFO @ Tue, 02 Aug 2022 11:01:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:43: #1 total tags in treatment: 10429191 INFO @ Tue, 02 Aug 2022 11:01:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:43: #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 11:01:43: #1 tags after filtering in treatment: 10429191 INFO @ Tue, 02 Aug 2022 11:01:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:43: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:44: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 11:01:44: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 11:01:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:44: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:44: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:44: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:44: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:01:44: #2 alternative fragment length(s) may be 4,73,566,570,574 bps INFO @ Tue, 02 Aug 2022 11:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.05_model.r WARNING @ Tue, 02 Aug 2022 11:01:44: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:01:44: #2 You may need to consider one of the other alternative d(s): 4,73,566,570,574 WARNING @ Tue, 02 Aug 2022 11:01:44: #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 11:01:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:45: 6000000 INFO @ Tue, 02 Aug 2022 11:01:46: 2000000 INFO @ Tue, 02 Aug 2022 11:01:53: 7000000 INFO @ Tue, 02 Aug 2022 11:01:53: 3000000 INFO @ Tue, 02 Aug 2022 11:02:00: 8000000 INFO @ Tue, 02 Aug 2022 11:02:00: 4000000 INFO @ Tue, 02 Aug 2022 11:02:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:02:07: 9000000 INFO @ Tue, 02 Aug 2022 11:02:08: 5000000 INFO @ Tue, 02 Aug 2022 11:02:14: 10000000 INFO @ Tue, 02 Aug 2022 11:02:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.05_summits.bed INFO @ Tue, 02 Aug 2022 11:02:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:02:15: 6000000 INFO @ Tue, 02 Aug 2022 11:02:17: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:02:17: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:02:17: #1 total tags in treatment: 10429191 INFO @ Tue, 02 Aug 2022 11:02:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:02:17: #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 11:02:18: #1 tags after filtering in treatment: 10429191 INFO @ Tue, 02 Aug 2022 11:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:02:18: #1 finished! INFO @ Tue, 02 Aug 2022 11:02:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:02:18: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 11:02:18: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 11:02:18: start model_add_line... INFO @ Tue, 02 Aug 2022 11:02:18: start X-correlation... INFO @ Tue, 02 Aug 2022 11:02:18: end of X-cor INFO @ Tue, 02 Aug 2022 11:02:18: #2 finished! INFO @ Tue, 02 Aug 2022 11:02:18: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:02:18: #2 alternative fragment length(s) may be 4,73,566,570,574 bps INFO @ Tue, 02 Aug 2022 11:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.10_model.r WARNING @ Tue, 02 Aug 2022 11:02:18: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:02:18: #2 You may need to consider one of the other alternative d(s): 4,73,566,570,574 WARNING @ Tue, 02 Aug 2022 11:02:18: #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 11:02:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:02:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:02:21: 7000000 INFO @ Tue, 02 Aug 2022 11:02:27: 8000000 INFO @ Tue, 02 Aug 2022 11:02:33: 9000000 INFO @ Tue, 02 Aug 2022 11:02:38: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:02:40: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:02:42: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:02:42: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:02:42: #1 total tags in treatment: 10429191 INFO @ Tue, 02 Aug 2022 11:02:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:02:42: #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 11:02:42: #1 tags after filtering in treatment: 10429191 INFO @ Tue, 02 Aug 2022 11:02:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:02:42: #1 finished! INFO @ Tue, 02 Aug 2022 11:02:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:02:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:02:43: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 11:02:43: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 11:02:43: start model_add_line... INFO @ Tue, 02 Aug 2022 11:02:43: start X-correlation... INFO @ Tue, 02 Aug 2022 11:02:43: end of X-cor INFO @ Tue, 02 Aug 2022 11:02:43: #2 finished! INFO @ Tue, 02 Aug 2022 11:02:43: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:02:43: #2 alternative fragment length(s) may be 4,73,566,570,574 bps INFO @ Tue, 02 Aug 2022 11:02:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.20_model.r WARNING @ Tue, 02 Aug 2022 11:02:43: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:02:43: #2 You may need to consider one of the other alternative d(s): 4,73,566,570,574 WARNING @ Tue, 02 Aug 2022 11:02:43: #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 11:02:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.10_summits.bed INFO @ Tue, 02 Aug 2022 11:02:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:03:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110375/SRX13110375.20_summits.bed INFO @ Tue, 02 Aug 2022 11:03:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling