Job ID = 16435592 SRX = SRX13110374 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:51:29 prefetch.2.10.7: 1) Downloading 'SRR16918044'... 2022-08-02T01:51:29 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:51:52 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:51:53 prefetch.2.10.7: 'SRR16918044' is valid 2022-08-02T01:51:53 prefetch.2.10.7: 1) 'SRR16918044' was downloaded successfully 2022-08-02T01:51:53 prefetch.2.10.7: 'SRR16918044' has 0 unresolved dependencies Read 13998882 spots for SRR16918044/SRR16918044.sra Written 13998882 spots for SRR16918044/SRR16918044.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436158 ("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: 00:04:07 13998882 reads; of these: 13998882 (100.00%) were unpaired; of these: 1708663 (12.21%) aligned 0 times 10596280 (75.69%) aligned exactly 1 time 1693939 (12.10%) aligned >1 times 87.79% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 2148960 / 12290219 = 0.1749 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 10:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.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 10:59:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:59:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:59:58: 1000000 INFO @ Tue, 02 Aug 2022 11:00:05: 2000000 INFO @ Tue, 02 Aug 2022 11:00:12: 3000000 INFO @ Tue, 02 Aug 2022 11:00:19: 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 11:00:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.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 11:00:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:26: 5000000 INFO @ Tue, 02 Aug 2022 11:00:28: 1000000 INFO @ Tue, 02 Aug 2022 11:00:33: 6000000 INFO @ Tue, 02 Aug 2022 11:00:34: 2000000 INFO @ Tue, 02 Aug 2022 11:00:41: 7000000 INFO @ Tue, 02 Aug 2022 11:00:41: 3000000 INFO @ Tue, 02 Aug 2022 11:00:48: 4000000 INFO @ Tue, 02 Aug 2022 11:00:48: 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 11:00:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.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 11:00:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:54: 5000000 INFO @ Tue, 02 Aug 2022 11:00:55: 9000000 INFO @ Tue, 02 Aug 2022 11:00:58: 1000000 INFO @ Tue, 02 Aug 2022 11:01:00: 6000000 INFO @ Tue, 02 Aug 2022 11:01:03: 10000000 INFO @ Tue, 02 Aug 2022 11:01:04: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:04: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:04: #1 total tags in treatment: 10141259 INFO @ Tue, 02 Aug 2022 11:01:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:04: #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 11:01:04: #1 tags after filtering in treatment: 10141259 INFO @ Tue, 02 Aug 2022 11:01:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:04: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:04: 2000000 INFO @ Tue, 02 Aug 2022 11:01:05: #2 number of paired peaks: 255 WARNING @ Tue, 02 Aug 2022 11:01:05: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Tue, 02 Aug 2022 11:01:05: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:05: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:05: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:05: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:05: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:01:05: #2 alternative fragment length(s) may be 4,72,544 bps INFO @ Tue, 02 Aug 2022 11:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.05_model.r WARNING @ Tue, 02 Aug 2022 11:01:05: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:01:05: #2 You may need to consider one of the other alternative d(s): 4,72,544 WARNING @ Tue, 02 Aug 2022 11:01:05: #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 11:01:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:07: 7000000 INFO @ Tue, 02 Aug 2022 11:01:11: 3000000 INFO @ Tue, 02 Aug 2022 11:01:13: 8000000 INFO @ Tue, 02 Aug 2022 11:01:17: 4000000 INFO @ Tue, 02 Aug 2022 11:01:20: 9000000 INFO @ Tue, 02 Aug 2022 11:01:23: 5000000 INFO @ Tue, 02 Aug 2022 11:01:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:01:26: 10000000 INFO @ Tue, 02 Aug 2022 11:01:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:27: #1 total tags in treatment: 10141259 INFO @ Tue, 02 Aug 2022 11:01:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:27: #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 11:01:27: #1 tags after filtering in treatment: 10141259 INFO @ Tue, 02 Aug 2022 11:01:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:27: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:28: #2 number of paired peaks: 255 WARNING @ Tue, 02 Aug 2022 11:01:28: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Tue, 02 Aug 2022 11:01:28: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:28: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:28: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:28: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:28: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:01:28: #2 alternative fragment length(s) may be 4,72,544 bps INFO @ Tue, 02 Aug 2022 11:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.10_model.r WARNING @ Tue, 02 Aug 2022 11:01:28: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:01:28: #2 You may need to consider one of the other alternative d(s): 4,72,544 WARNING @ Tue, 02 Aug 2022 11:01:28: #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 11:01:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:30: 6000000 INFO @ Tue, 02 Aug 2022 11:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.05_summits.bed INFO @ Tue, 02 Aug 2022 11:01:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (657 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:01:36: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:01:42: 8000000 INFO @ Tue, 02 Aug 2022 11:01:48: 9000000 INFO @ Tue, 02 Aug 2022 11:01:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:01:54: 10000000 INFO @ Tue, 02 Aug 2022 11:01:54: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:01:54: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:01:54: #1 total tags in treatment: 10141259 INFO @ Tue, 02 Aug 2022 11:01:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:54: #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 11:01:55: #1 tags after filtering in treatment: 10141259 INFO @ Tue, 02 Aug 2022 11:01:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:01:55: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:55: #2 number of paired peaks: 255 WARNING @ Tue, 02 Aug 2022 11:01:55: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Tue, 02 Aug 2022 11:01:55: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:55: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:55: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:55: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:55: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:01:55: #2 alternative fragment length(s) may be 4,72,544 bps INFO @ Tue, 02 Aug 2022 11:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.20_model.r WARNING @ Tue, 02 Aug 2022 11:01:55: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:01:55: #2 You may need to consider one of the other alternative d(s): 4,72,544 WARNING @ Tue, 02 Aug 2022 11:01:55: #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 11:01:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:01:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:01:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.10_summits.bed INFO @ Tue, 02 Aug 2022 11:01:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (365 records, 4 fields): 99 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:02:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:02:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:02:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:02:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110374/SRX13110374.20_summits.bed INFO @ Tue, 02 Aug 2022 11:02:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 28 millis CompletedMACS2peakCalling