Job ID = 14157930 SRX = SRX10641200 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T03:52:19 prefetch.2.10.7: 1) Downloading 'SRR14280078'... 2021-12-08T03:52:19 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T03:55:34 prefetch.2.10.7: HTTPS download succeed 2021-12-08T03:55:34 prefetch.2.10.7: 1) 'SRR14280078' was downloaded successfully 2021-12-08T03:55:34 prefetch.2.10.7: 'SRR14280078' has 0 unresolved dependencies Read 21881466 spots for SRR14280078/SRR14280078.sra Written 21881466 spots for SRR14280078/SRR14280078.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158198 ("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: 00:19:40 21881466 reads; of these: 21881466 (100.00%) were paired; of these: 17511975 (80.03%) aligned concordantly 0 times 3095854 (14.15%) aligned concordantly exactly 1 time 1273637 (5.82%) aligned concordantly >1 times ---- 17511975 pairs aligned concordantly 0 times; of these: 1350332 (7.71%) aligned discordantly 1 time ---- 16161643 pairs aligned 0 times concordantly or discordantly; of these: 32323286 mates make up the pairs; of these: 31676735 (98.00%) aligned 0 times 333777 (1.03%) aligned exactly 1 time 312774 (0.97%) aligned >1 times 27.62% overall alignment rate Time searching: 00:19:40 Overall time: 00:19:40 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1055911 / 5688864 = 0.1856 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 13:23:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.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 13:23:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:23:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:23:52: 1000000 INFO @ Wed, 08 Dec 2021 13:24:01: 2000000 INFO @ Wed, 08 Dec 2021 13:24:10: 3000000 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 13:24:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.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 13:24:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:24:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:24:19: 4000000 INFO @ Wed, 08 Dec 2021 13:24:24: 1000000 INFO @ Wed, 08 Dec 2021 13:24:30: 5000000 INFO @ Wed, 08 Dec 2021 13:24:34: 2000000 INFO @ Wed, 08 Dec 2021 13:24:40: 6000000 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 13:24:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.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 13:24:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:24:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:24:45: 3000000 INFO @ Wed, 08 Dec 2021 13:24:51: 7000000 INFO @ Wed, 08 Dec 2021 13:24:54: 1000000 INFO @ Wed, 08 Dec 2021 13:24:55: 4000000 INFO @ Wed, 08 Dec 2021 13:25:01: 8000000 INFO @ Wed, 08 Dec 2021 13:25:05: 2000000 INFO @ Wed, 08 Dec 2021 13:25:06: 5000000 INFO @ Wed, 08 Dec 2021 13:25:12: 9000000 INFO @ Wed, 08 Dec 2021 13:25:15: 3000000 INFO @ Wed, 08 Dec 2021 13:25:16: 6000000 INFO @ Wed, 08 Dec 2021 13:25:23: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:25:23: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:25:23: #1 total tags in treatment: 3484547 INFO @ Wed, 08 Dec 2021 13:25:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:25:23: #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 13:25:23: #1 tags after filtering in treatment: 2887937 INFO @ Wed, 08 Dec 2021 13:25:23: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 08 Dec 2021 13:25:23: #1 finished! INFO @ Wed, 08 Dec 2021 13:25:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:25:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:25:23: #2 number of paired peaks: 845 WARNING @ Wed, 08 Dec 2021 13:25:23: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Wed, 08 Dec 2021 13:25:23: start model_add_line... INFO @ Wed, 08 Dec 2021 13:25:23: start X-correlation... INFO @ Wed, 08 Dec 2021 13:25:23: end of X-cor INFO @ Wed, 08 Dec 2021 13:25:23: #2 finished! INFO @ Wed, 08 Dec 2021 13:25:23: #2 predicted fragment length is 243 bps INFO @ Wed, 08 Dec 2021 13:25:23: #2 alternative fragment length(s) may be 243 bps INFO @ Wed, 08 Dec 2021 13:25:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.05_model.r WARNING @ Wed, 08 Dec 2021 13:25:23: #2 Since the d (243) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:25:23: #2 You may need to consider one of the other alternative d(s): 243 WARNING @ Wed, 08 Dec 2021 13:25:23: #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 13:25:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:25:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:25:25: 4000000 INFO @ Wed, 08 Dec 2021 13:25:27: 7000000 INFO @ Wed, 08 Dec 2021 13:25:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:25:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.05_summits.bed INFO @ Wed, 08 Dec 2021 13:25:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1231 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:25:35: 5000000 INFO @ Wed, 08 Dec 2021 13:25:37: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:25:45: 6000000 INFO @ Wed, 08 Dec 2021 13:25:48: 9000000 INFO @ Wed, 08 Dec 2021 13:25:56: 7000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:25:59: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:25:59: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:25:59: #1 total tags in treatment: 3484547 INFO @ Wed, 08 Dec 2021 13:25:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:25:59: #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 13:25:59: #1 tags after filtering in treatment: 2887937 INFO @ Wed, 08 Dec 2021 13:25:59: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 08 Dec 2021 13:25:59: #1 finished! INFO @ Wed, 08 Dec 2021 13:25:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:25:59: #2 number of paired peaks: 845 WARNING @ Wed, 08 Dec 2021 13:25:59: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Wed, 08 Dec 2021 13:25:59: start model_add_line... INFO @ Wed, 08 Dec 2021 13:25:59: start X-correlation... INFO @ Wed, 08 Dec 2021 13:25:59: end of X-cor INFO @ Wed, 08 Dec 2021 13:25:59: #2 finished! INFO @ Wed, 08 Dec 2021 13:25:59: #2 predicted fragment length is 243 bps INFO @ Wed, 08 Dec 2021 13:25:59: #2 alternative fragment length(s) may be 243 bps INFO @ Wed, 08 Dec 2021 13:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.10_model.r WARNING @ Wed, 08 Dec 2021 13:25:59: #2 Since the d (243) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:25:59: #2 You may need to consider one of the other alternative d(s): 243 WARNING @ Wed, 08 Dec 2021 13:25:59: #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 13:25:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:26:06: 8000000 INFO @ Wed, 08 Dec 2021 13:26:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:26:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:26:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:26:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.10_summits.bed INFO @ Wed, 08 Dec 2021 13:26:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:26:16: 9000000 INFO @ Wed, 08 Dec 2021 13:26:25: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:26:25: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:26:25: #1 total tags in treatment: 3484547 INFO @ Wed, 08 Dec 2021 13:26:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:26:25: #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 13:26:25: #1 tags after filtering in treatment: 2887937 INFO @ Wed, 08 Dec 2021 13:26:25: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 08 Dec 2021 13:26:25: #1 finished! INFO @ Wed, 08 Dec 2021 13:26:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:26:25: #2 number of paired peaks: 845 WARNING @ Wed, 08 Dec 2021 13:26:25: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Wed, 08 Dec 2021 13:26:25: start model_add_line... INFO @ Wed, 08 Dec 2021 13:26:25: start X-correlation... INFO @ Wed, 08 Dec 2021 13:26:25: end of X-cor INFO @ Wed, 08 Dec 2021 13:26:25: #2 finished! INFO @ Wed, 08 Dec 2021 13:26:25: #2 predicted fragment length is 243 bps INFO @ Wed, 08 Dec 2021 13:26:25: #2 alternative fragment length(s) may be 243 bps INFO @ Wed, 08 Dec 2021 13:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.20_model.r WARNING @ Wed, 08 Dec 2021 13:26:25: #2 Since the d (243) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:26:25: #2 You may need to consider one of the other alternative d(s): 243 WARNING @ Wed, 08 Dec 2021 13:26:25: #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 13:26:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:26:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641200/SRX10641200.20_summits.bed INFO @ Wed, 08 Dec 2021 13:26:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 1 millis CompletedMACS2peakCalling