Job ID = 16435142 SRX = SRX13110340 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:37:45 prefetch.2.10.7: 1) Downloading 'SRR16918010'... 2022-08-02T01:37:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:38:16 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:38:17 prefetch.2.10.7: 'SRR16918010' is valid 2022-08-02T01:38:17 prefetch.2.10.7: 1) 'SRR16918010' was downloaded successfully 2022-08-02T01:38:17 prefetch.2.10.7: 'SRR16918010' has 0 unresolved dependencies Read 17216894 spots for SRR16918010/SRR16918010.sra Written 17216894 spots for SRR16918010/SRR16918010.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435539 ("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: 00:05:48 17216894 reads; of these: 17216894 (100.00%) were unpaired; of these: 2927566 (17.00%) aligned 0 times 12176670 (70.73%) aligned exactly 1 time 2112658 (12.27%) aligned >1 times 83.00% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 7715528 / 14289328 = 0.5400 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 10:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.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 10:49:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:49:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:49:46: 1000000 INFO @ Tue, 02 Aug 2022 10:49:53: 2000000 INFO @ Tue, 02 Aug 2022 10:50:01: 3000000 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 10:50:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.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 10:50:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:09: 4000000 INFO @ Tue, 02 Aug 2022 10:50:15: 1000000 INFO @ Tue, 02 Aug 2022 10:50:17: 5000000 INFO @ Tue, 02 Aug 2022 10:50:23: 2000000 INFO @ Tue, 02 Aug 2022 10:50:26: 6000000 INFO @ Tue, 02 Aug 2022 10:50:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:50:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:50:30: #1 total tags in treatment: 6573800 INFO @ Tue, 02 Aug 2022 10:50:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:50:30: #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 10:50:30: #1 tags after filtering in treatment: 6573800 INFO @ Tue, 02 Aug 2022 10:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:50:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:50:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:50:31: #2 number of paired peaks: 438 WARNING @ Tue, 02 Aug 2022 10:50:31: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 02 Aug 2022 10:50:31: start model_add_line... INFO @ Tue, 02 Aug 2022 10:50:31: start X-correlation... INFO @ Tue, 02 Aug 2022 10:50:31: end of X-cor INFO @ Tue, 02 Aug 2022 10:50:31: #2 finished! INFO @ Tue, 02 Aug 2022 10:50:31: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:50:31: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:50:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.05_model.r WARNING @ Tue, 02 Aug 2022 10:50:31: #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 10:50:31: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:50:31: #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 10:50:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:50:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:50:31: 3000000 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 10:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.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 10:50:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:40: 4000000 INFO @ Tue, 02 Aug 2022 10:50:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:50:45: 1000000 INFO @ Tue, 02 Aug 2022 10:50:48: 5000000 INFO @ Tue, 02 Aug 2022 10:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.05_summits.bed INFO @ Tue, 02 Aug 2022 10:50:51: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (607 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:50:53: 2000000 INFO @ Tue, 02 Aug 2022 10:50:56: 6000000 INFO @ Tue, 02 Aug 2022 10:51:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:51:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:51:01: #1 total tags in treatment: 6573800 INFO @ Tue, 02 Aug 2022 10:51:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:51:01: #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 10:51:01: #1 tags after filtering in treatment: 6573800 INFO @ Tue, 02 Aug 2022 10:51:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:51:01: #1 finished! INFO @ Tue, 02 Aug 2022 10:51:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:51:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:51:01: 3000000 INFO @ Tue, 02 Aug 2022 10:51:01: #2 number of paired peaks: 438 WARNING @ Tue, 02 Aug 2022 10:51:01: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 02 Aug 2022 10:51:01: start model_add_line... INFO @ Tue, 02 Aug 2022 10:51:01: start X-correlation... INFO @ Tue, 02 Aug 2022 10:51:02: end of X-cor INFO @ Tue, 02 Aug 2022 10:51:02: #2 finished! INFO @ Tue, 02 Aug 2022 10:51:02: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:51:02: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.10_model.r WARNING @ Tue, 02 Aug 2022 10:51:02: #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 10:51:02: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:51:02: #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 10:51:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:51:09: 4000000 INFO @ Tue, 02 Aug 2022 10:51:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:51:17: 5000000 INFO @ Tue, 02 Aug 2022 10:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.10_summits.bed INFO @ Tue, 02 Aug 2022 10:51:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:51:25: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:51:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:51:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:51:30: #1 total tags in treatment: 6573800 INFO @ Tue, 02 Aug 2022 10:51:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:51:30: #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 10:51:30: #1 tags after filtering in treatment: 6573800 INFO @ Tue, 02 Aug 2022 10:51:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:51:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:51:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:51:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:51:30: #2 number of paired peaks: 438 WARNING @ Tue, 02 Aug 2022 10:51:30: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 02 Aug 2022 10:51:30: start model_add_line... INFO @ Tue, 02 Aug 2022 10:51:30: start X-correlation... INFO @ Tue, 02 Aug 2022 10:51:30: end of X-cor INFO @ Tue, 02 Aug 2022 10:51:30: #2 finished! INFO @ Tue, 02 Aug 2022 10:51:30: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:51:30: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:51:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.20_model.r WARNING @ Tue, 02 Aug 2022 10:51:30: #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 10:51:30: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:51:30: #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 10:51:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:51:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:51:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110340/SRX13110340.20_summits.bed INFO @ Tue, 02 Aug 2022 10:51:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 18 millis CompletedMACS2peakCalling