Job ID = 16435594 SRX = SRX13110376 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 'SRR16918046'... 2022-08-02T01:52:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:52:25 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:52:25 prefetch.2.10.7: 'SRR16918046' is valid 2022-08-02T01:52:25 prefetch.2.10.7: 1) 'SRR16918046' was downloaded successfully 2022-08-02T01:52:25 prefetch.2.10.7: 'SRR16918046' has 0 unresolved dependencies Read 12806778 spots for SRR16918046/SRR16918046.sra Written 12806778 spots for SRR16918046/SRR16918046.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436153 ("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: 00:02:09 12806778 reads; of these: 12806778 (100.00%) were unpaired; of these: 9350350 (73.01%) aligned 0 times 2954726 (23.07%) aligned exactly 1 time 501702 (3.92%) aligned >1 times 26.99% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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_rmdupse_core] 340191 / 3456428 = 0.0984 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 10:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.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 10:57:02: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:57:02: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:10: 1000000 INFO @ Tue, 02 Aug 2022 10:57:19: 2000000 INFO @ Tue, 02 Aug 2022 10:57:26: 3000000 INFO @ Tue, 02 Aug 2022 10:57:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:27: #1 total tags in treatment: 3116237 INFO @ Tue, 02 Aug 2022 10:57:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:27: #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 10:57:27: #1 tags after filtering in treatment: 3116237 INFO @ Tue, 02 Aug 2022 10:57:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:27: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:27: #2 number of paired peaks: 291 WARNING @ Tue, 02 Aug 2022 10:57:27: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 02 Aug 2022 10:57:27: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:27: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:27: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:27: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:27: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:57:27: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 10:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.05_model.r WARNING @ Tue, 02 Aug 2022 10:57:27: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:57:27: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 10:57:27: #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 10:57:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:27: #3 Pre-compute pvalue-qvalue table... 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 10:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.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 10:57:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:57:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:57:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:57:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:57:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:57:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.05_summits.bed INFO @ Tue, 02 Aug 2022 10:57:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:57:38: 1000000 INFO @ Tue, 02 Aug 2022 10:57:45: 2000000 INFO @ Tue, 02 Aug 2022 10:57:53: 3000000 INFO @ Tue, 02 Aug 2022 10:57:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:57:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:57:53: #1 total tags in treatment: 3116237 INFO @ Tue, 02 Aug 2022 10:57:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:57:53: #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 10:57:53: #1 tags after filtering in treatment: 3116237 INFO @ Tue, 02 Aug 2022 10:57:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:57:53: #1 finished! INFO @ Tue, 02 Aug 2022 10:57:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:57:54: #2 number of paired peaks: 291 WARNING @ Tue, 02 Aug 2022 10:57:54: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 02 Aug 2022 10:57:54: start model_add_line... INFO @ Tue, 02 Aug 2022 10:57:54: start X-correlation... INFO @ Tue, 02 Aug 2022 10:57:54: end of X-cor INFO @ Tue, 02 Aug 2022 10:57:54: #2 finished! INFO @ Tue, 02 Aug 2022 10:57:54: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:57:54: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 10:57:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.10_model.r WARNING @ Tue, 02 Aug 2022 10:57:54: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:57:54: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 10:57:54: #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 10:57:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:57:54: #3 Pre-compute pvalue-qvalue table... 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 10:58:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:58:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.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 10:58:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:58:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:58:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.10_summits.bed INFO @ Tue, 02 Aug 2022 10:58:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:58:07: 1000000 INFO @ Tue, 02 Aug 2022 10:58:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:58:21: 3000000 INFO @ Tue, 02 Aug 2022 10:58:21: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:58:21: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:58:21: #1 total tags in treatment: 3116237 INFO @ Tue, 02 Aug 2022 10:58:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:58:21: #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 10:58:22: #1 tags after filtering in treatment: 3116237 INFO @ Tue, 02 Aug 2022 10:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:58:22: #1 finished! INFO @ Tue, 02 Aug 2022 10:58:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:58:22: #2 number of paired peaks: 291 WARNING @ Tue, 02 Aug 2022 10:58:22: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 02 Aug 2022 10:58:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:58:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:58:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:58:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:58:22: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:58:22: #2 alternative fragment length(s) may be 74 bps INFO @ Tue, 02 Aug 2022 10:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.20_model.r WARNING @ Tue, 02 Aug 2022 10:58:22: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:58:22: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Tue, 02 Aug 2022 10:58:22: #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 10:58:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:58:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110376/SRX13110376.20_summits.bed INFO @ Tue, 02 Aug 2022 10:58:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 16 millis CompletedMACS2peakCalling