Job ID = 14159372 SRX = SRX3180826 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14784189 spots for SRR6030477/SRR6030477.sra Written 14784189 spots for SRR6030477/SRR6030477.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159566 ("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: 00:03:09 14784189 reads; of these: 14784189 (100.00%) were unpaired; of these: 1406999 (9.52%) aligned 0 times 10392861 (70.30%) aligned exactly 1 time 2984329 (20.19%) aligned >1 times 90.48% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2770522 / 13377190 = 0.2071 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 @ Wed, 08 Dec 2021 21:24:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.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 @ Wed, 08 Dec 2021 21:24:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:24:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:24:38: 1000000 INFO @ Wed, 08 Dec 2021 21:24:44: 2000000 INFO @ Wed, 08 Dec 2021 21:24:49: 3000000 INFO @ Wed, 08 Dec 2021 21:24:55: 4000000 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 @ Wed, 08 Dec 2021 21:25:01: 5000000 INFO @ Wed, 08 Dec 2021 21:25:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.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 @ Wed, 08 Dec 2021 21:25:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:25:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:25:07: 6000000 INFO @ Wed, 08 Dec 2021 21:25:09: 1000000 INFO @ Wed, 08 Dec 2021 21:25:14: 7000000 INFO @ Wed, 08 Dec 2021 21:25:15: 2000000 INFO @ Wed, 08 Dec 2021 21:25:21: 8000000 INFO @ Wed, 08 Dec 2021 21:25:22: 3000000 INFO @ Wed, 08 Dec 2021 21:25:27: 9000000 INFO @ Wed, 08 Dec 2021 21:25:29: 4000000 BedGraph に変換中... 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 @ Wed, 08 Dec 2021 21:25:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.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 @ Wed, 08 Dec 2021 21:25:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:25:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:25:34: 10000000 INFO @ Wed, 08 Dec 2021 21:25:36: 5000000 INFO @ Wed, 08 Dec 2021 21:25:38: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:25:38: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:25:38: #1 total tags in treatment: 10606668 INFO @ Wed, 08 Dec 2021 21:25:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:25:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:25:38: #1 tags after filtering in treatment: 10606668 INFO @ Wed, 08 Dec 2021 21:25:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:25:38: #1 finished! INFO @ Wed, 08 Dec 2021 21:25:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:25:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:25:39: #2 number of paired peaks: 484 WARNING @ Wed, 08 Dec 2021 21:25:39: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Wed, 08 Dec 2021 21:25:39: start model_add_line... INFO @ Wed, 08 Dec 2021 21:25:39: start X-correlation... INFO @ Wed, 08 Dec 2021 21:25:39: end of X-cor INFO @ Wed, 08 Dec 2021 21:25:39: #2 finished! INFO @ Wed, 08 Dec 2021 21:25:39: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 21:25:39: #2 alternative fragment length(s) may be 2,47 bps INFO @ Wed, 08 Dec 2021 21:25:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.05_model.r WARNING @ Wed, 08 Dec 2021 21:25:39: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:25:39: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Wed, 08 Dec 2021 21:25:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:25:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:25:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:25:40: 1000000 INFO @ Wed, 08 Dec 2021 21:25:43: 6000000 INFO @ Wed, 08 Dec 2021 21:25:48: 2000000 INFO @ Wed, 08 Dec 2021 21:25:50: 7000000 INFO @ Wed, 08 Dec 2021 21:25:57: 3000000 INFO @ Wed, 08 Dec 2021 21:25:58: 8000000 INFO @ Wed, 08 Dec 2021 21:25:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:26:05: 4000000 INFO @ Wed, 08 Dec 2021 21:26:05: 9000000 INFO @ Wed, 08 Dec 2021 21:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.05_summits.bed INFO @ Wed, 08 Dec 2021 21:26:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (640 records, 4 fields): 116 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:26:12: 10000000 INFO @ Wed, 08 Dec 2021 21:26:13: 5000000 INFO @ Wed, 08 Dec 2021 21:26:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:26:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:26:17: #1 total tags in treatment: 10606668 INFO @ Wed, 08 Dec 2021 21:26:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:26:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:26:17: #1 tags after filtering in treatment: 10606668 INFO @ Wed, 08 Dec 2021 21:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:26:17: #1 finished! INFO @ Wed, 08 Dec 2021 21:26:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:26:17: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 21:26:18: #2 number of paired peaks: 484 BigWig に変換中... WARNING @ Wed, 08 Dec 2021 21:26:18: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Wed, 08 Dec 2021 21:26:18: start model_add_line... INFO @ Wed, 08 Dec 2021 21:26:18: start X-correlation... INFO @ Wed, 08 Dec 2021 21:26:18: end of X-cor INFO @ Wed, 08 Dec 2021 21:26:18: #2 finished! INFO @ Wed, 08 Dec 2021 21:26:18: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 21:26:18: #2 alternative fragment length(s) may be 2,47 bps INFO @ Wed, 08 Dec 2021 21:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.10_model.r WARNING @ Wed, 08 Dec 2021 21:26:18: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:26:18: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Wed, 08 Dec 2021 21:26:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:26:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:26:20: 6000000 INFO @ Wed, 08 Dec 2021 21:26:27: 7000000 INFO @ Wed, 08 Dec 2021 21:26:34: 8000000 INFO @ Wed, 08 Dec 2021 21:26:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:26:41: 9000000 INFO @ Wed, 08 Dec 2021 21:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.10_summits.bed INFO @ Wed, 08 Dec 2021 21:26:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:26:49: 10000000 INFO @ Wed, 08 Dec 2021 21:26:53: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 21:26:53: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 21:26:53: #1 total tags in treatment: 10606668 INFO @ Wed, 08 Dec 2021 21:26:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:26:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:26:54: #1 tags after filtering in treatment: 10606668 INFO @ Wed, 08 Dec 2021 21:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:26:54: #1 finished! INFO @ Wed, 08 Dec 2021 21:26:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:26:54: #2 number of paired peaks: 484 WARNING @ Wed, 08 Dec 2021 21:26:54: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Wed, 08 Dec 2021 21:26:54: start model_add_line... INFO @ Wed, 08 Dec 2021 21:26:54: start X-correlation... INFO @ Wed, 08 Dec 2021 21:26:54: end of X-cor INFO @ Wed, 08 Dec 2021 21:26:54: #2 finished! INFO @ Wed, 08 Dec 2021 21:26:54: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 21:26:54: #2 alternative fragment length(s) may be 2,47 bps INFO @ Wed, 08 Dec 2021 21:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.20_model.r WARNING @ Wed, 08 Dec 2021 21:26:54: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:26:54: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Wed, 08 Dec 2021 21:26:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:26:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:27:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180826/SRX3180826.20_summits.bed INFO @ Wed, 08 Dec 2021 21:27:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (153 records, 4 fields): 1 millis CompletedMACS2peakCalling