Job ID = 16435130 SRX = SRX13110339 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:35:32 prefetch.2.10.7: 1) Downloading 'SRR16918009'... 2022-08-02T01:35:32 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:36:06 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:36:06 prefetch.2.10.7: 'SRR16918009' is valid 2022-08-02T01:36:06 prefetch.2.10.7: 1) 'SRR16918009' was downloaded successfully 2022-08-02T01:36:07 prefetch.2.10.7: 'SRR16918009' has 0 unresolved dependencies Read 18102473 spots for SRR16918009/SRR16918009.sra Written 18102473 spots for SRR16918009/SRR16918009.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435512 ("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: 00:03:41 18102473 reads; of these: 18102473 (100.00%) were unpaired; of these: 9497530 (52.47%) aligned 0 times 7414317 (40.96%) aligned exactly 1 time 1190626 (6.58%) aligned >1 times 47.53% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 5088109 / 8604943 = 0.5913 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 10:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.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 10:42:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:42:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:02: 1000000 INFO @ Tue, 02 Aug 2022 10:43:08: 2000000 INFO @ Tue, 02 Aug 2022 10:43:14: 3000000 INFO @ Tue, 02 Aug 2022 10:43:16: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:43:16: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:43:16: #1 total tags in treatment: 3516834 INFO @ Tue, 02 Aug 2022 10:43:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:43:16: #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 10:43:16: #1 tags after filtering in treatment: 3516834 INFO @ Tue, 02 Aug 2022 10:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:43:16: #1 finished! INFO @ Tue, 02 Aug 2022 10:43:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:43:17: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:43:17: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:43:17: start model_add_line... INFO @ Tue, 02 Aug 2022 10:43:17: start X-correlation... INFO @ Tue, 02 Aug 2022 10:43:17: end of X-cor INFO @ Tue, 02 Aug 2022 10:43:17: #2 finished! INFO @ Tue, 02 Aug 2022 10:43:17: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:43:17: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 10:43:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.05_model.r WARNING @ Tue, 02 Aug 2022 10:43:17: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:43:17: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 10:43:17: #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 10:43:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:43:17: #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 10:43:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.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 10:43:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:43:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:43:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:43:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.05_summits.bed INFO @ Tue, 02 Aug 2022 10:43:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 87 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:43:32: 1000000 INFO @ Tue, 02 Aug 2022 10:43:38: 2000000 INFO @ Tue, 02 Aug 2022 10:43:44: 3000000 INFO @ Tue, 02 Aug 2022 10:43:47: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:43:47: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:43:47: #1 total tags in treatment: 3516834 INFO @ Tue, 02 Aug 2022 10:43:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:43:47: #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 10:43:47: #1 tags after filtering in treatment: 3516834 INFO @ Tue, 02 Aug 2022 10:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:43:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:43:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:43:47: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:43:47: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:43:47: start model_add_line... INFO @ Tue, 02 Aug 2022 10:43:47: start X-correlation... INFO @ Tue, 02 Aug 2022 10:43:47: end of X-cor INFO @ Tue, 02 Aug 2022 10:43:47: #2 finished! INFO @ Tue, 02 Aug 2022 10:43:47: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:43:47: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 10:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.10_model.r WARNING @ Tue, 02 Aug 2022 10:43:47: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:43:47: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 10:43:47: #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 10:43:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:43:47: #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 10:43:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.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 10:43:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:43:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:43:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:43:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.10_summits.bed INFO @ Tue, 02 Aug 2022 10:43:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (327 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:44:02: 1000000 INFO @ Tue, 02 Aug 2022 10:44:09: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:44:16: 3000000 INFO @ Tue, 02 Aug 2022 10:44:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:44:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:44:20: #1 total tags in treatment: 3516834 INFO @ Tue, 02 Aug 2022 10:44:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:44:20: #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 10:44:20: #1 tags after filtering in treatment: 3516834 INFO @ Tue, 02 Aug 2022 10:44:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:44:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:44:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:44:20: #2 number of paired peaks: 439 WARNING @ Tue, 02 Aug 2022 10:44:20: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Tue, 02 Aug 2022 10:44:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:44:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:44:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:44:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:44:20: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:44:20: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 10:44:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.20_model.r WARNING @ Tue, 02 Aug 2022 10:44:20: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:44:20: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 10:44:20: #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 10:44:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:44:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:44:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:44:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:44:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:44:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110339/SRX13110339.20_summits.bed INFO @ Tue, 02 Aug 2022 10:44:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 16 millis CompletedMACS2peakCalling