Job ID = 14159673 SRX = SRX3180792 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7903471 spots for SRR6030443/SRR6030443.sra Written 7903471 spots for SRR6030443/SRR6030443.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160276 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:51 7903471 reads; of these: 7903471 (100.00%) were unpaired; of these: 411551 (5.21%) aligned 0 times 6149501 (77.81%) aligned exactly 1 time 1342419 (16.99%) aligned >1 times 94.79% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 559971 / 7491920 = 0.0747 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.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 @ Thu, 09 Dec 2021 00:18:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:18:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:18:09: 1000000 INFO @ Thu, 09 Dec 2021 00:18:14: 2000000 INFO @ Thu, 09 Dec 2021 00:18:19: 3000000 INFO @ Thu, 09 Dec 2021 00:18:24: 4000000 INFO @ Thu, 09 Dec 2021 00:18:29: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.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 @ Thu, 09 Dec 2021 00:18:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:18:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:18:35: 6000000 INFO @ Thu, 09 Dec 2021 00:18:40: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:18:40: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:18:40: #1 total tags in treatment: 6931949 INFO @ Thu, 09 Dec 2021 00:18:40: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:18:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:18:40: 1000000 INFO @ Thu, 09 Dec 2021 00:18:40: #1 tags after filtering in treatment: 6931949 INFO @ Thu, 09 Dec 2021 00:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:18:40: #1 finished! INFO @ Thu, 09 Dec 2021 00:18:40: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:18:41: #2 number of paired peaks: 425 WARNING @ Thu, 09 Dec 2021 00:18:41: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 09 Dec 2021 00:18:41: start model_add_line... INFO @ Thu, 09 Dec 2021 00:18:41: start X-correlation... INFO @ Thu, 09 Dec 2021 00:18:41: end of X-cor INFO @ Thu, 09 Dec 2021 00:18:41: #2 finished! INFO @ Thu, 09 Dec 2021 00:18:41: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 00:18:41: #2 alternative fragment length(s) may be 4,51 bps INFO @ Thu, 09 Dec 2021 00:18:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.05_model.r WARNING @ Thu, 09 Dec 2021 00:18:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:18:41: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Thu, 09 Dec 2021 00:18:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:18:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:18:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:18:47: 2000000 INFO @ Thu, 09 Dec 2021 00:18:53: 3000000 INFO @ Thu, 09 Dec 2021 00:18:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:19:00: 4000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 00:19:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:19:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:19:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.05_summits.bed INFO @ Thu, 09 Dec 2021 00:19:01: Done! WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.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 @ Thu, 09 Dec 2021 00:19:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:19:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:19:06: 5000000 INFO @ Thu, 09 Dec 2021 00:19:09: 1000000 INFO @ Thu, 09 Dec 2021 00:19:13: 6000000 INFO @ Thu, 09 Dec 2021 00:19:15: 2000000 INFO @ Thu, 09 Dec 2021 00:19:19: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:19:19: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:19:19: #1 total tags in treatment: 6931949 INFO @ Thu, 09 Dec 2021 00:19:19: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:19:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:19:20: #1 tags after filtering in treatment: 6931949 INFO @ Thu, 09 Dec 2021 00:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:19:20: #1 finished! INFO @ Thu, 09 Dec 2021 00:19:20: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:19:20: #2 number of paired peaks: 425 WARNING @ Thu, 09 Dec 2021 00:19:20: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 09 Dec 2021 00:19:20: start model_add_line... INFO @ Thu, 09 Dec 2021 00:19:20: start X-correlation... INFO @ Thu, 09 Dec 2021 00:19:20: end of X-cor INFO @ Thu, 09 Dec 2021 00:19:20: #2 finished! INFO @ Thu, 09 Dec 2021 00:19:20: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 00:19:20: #2 alternative fragment length(s) may be 4,51 bps INFO @ Thu, 09 Dec 2021 00:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.10_model.r WARNING @ Thu, 09 Dec 2021 00:19:20: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:19:20: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Thu, 09 Dec 2021 00:19:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:19:20: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:19:21: 3000000 INFO @ Thu, 09 Dec 2021 00:19:27: 4000000 INFO @ Thu, 09 Dec 2021 00:19:32: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:19:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:19:38: 6000000 INFO @ Thu, 09 Dec 2021 00:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.10_summits.bed INFO @ Thu, 09 Dec 2021 00:19:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (374 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:19:43: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:19:43: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:19:43: #1 total tags in treatment: 6931949 INFO @ Thu, 09 Dec 2021 00:19:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:19:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:19:43: #1 tags after filtering in treatment: 6931949 INFO @ Thu, 09 Dec 2021 00:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:19:43: #1 finished! INFO @ Thu, 09 Dec 2021 00:19:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:19:44: #2 number of paired peaks: 425 WARNING @ Thu, 09 Dec 2021 00:19:44: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Thu, 09 Dec 2021 00:19:44: start model_add_line... INFO @ Thu, 09 Dec 2021 00:19:44: start X-correlation... INFO @ Thu, 09 Dec 2021 00:19:44: end of X-cor INFO @ Thu, 09 Dec 2021 00:19:44: #2 finished! INFO @ Thu, 09 Dec 2021 00:19:44: #2 predicted fragment length is 51 bps INFO @ Thu, 09 Dec 2021 00:19:44: #2 alternative fragment length(s) may be 4,51 bps INFO @ Thu, 09 Dec 2021 00:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.20_model.r WARNING @ Thu, 09 Dec 2021 00:19:44: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:19:44: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Thu, 09 Dec 2021 00:19:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:19:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:19:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:19:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180792/SRX3180792.20_summits.bed INFO @ Thu, 09 Dec 2021 00:20:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 1 millis CompletedMACS2peakCalling