Job ID = 14158406 SRX = SRX10641192 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22401560 spots for SRR14280086/SRR14280086.sra Written 22401560 spots for SRR14280086/SRR14280086.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159198 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:34:45 22401560 reads; of these: 22401560 (100.00%) were paired; of these: 14531319 (64.87%) aligned concordantly 0 times 4842464 (21.62%) aligned concordantly exactly 1 time 3027777 (13.52%) aligned concordantly >1 times ---- 14531319 pairs aligned concordantly 0 times; of these: 1736993 (11.95%) aligned discordantly 1 time ---- 12794326 pairs aligned 0 times concordantly or discordantly; of these: 25588652 mates make up the pairs; of these: 24644079 (96.31%) aligned 0 times 473244 (1.85%) aligned exactly 1 time 471329 (1.84%) aligned >1 times 44.99% overall alignment rate Time searching: 00:34:46 Overall time: 00:34:46 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 16 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] 2157635 / 9566768 = 0.2255 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 18:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.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 18:15:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:15:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:15:11: 1000000 INFO @ Wed, 08 Dec 2021 18:15:18: 2000000 INFO @ Wed, 08 Dec 2021 18:15:25: 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 18:15:32: 4000000 INFO @ Wed, 08 Dec 2021 18:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.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 18:15:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:15:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:15:40: 5000000 INFO @ Wed, 08 Dec 2021 18:15:41: 1000000 INFO @ Wed, 08 Dec 2021 18:15:47: 6000000 INFO @ Wed, 08 Dec 2021 18:15:49: 2000000 INFO @ Wed, 08 Dec 2021 18:15:55: 7000000 INFO @ Wed, 08 Dec 2021 18:15:56: 3000000 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 18:16:02: 8000000 INFO @ Wed, 08 Dec 2021 18:16:04: 4000000 INFO @ Wed, 08 Dec 2021 18:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.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 18:16:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:16:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:16:10: 9000000 INFO @ Wed, 08 Dec 2021 18:16:11: 5000000 INFO @ Wed, 08 Dec 2021 18:16:11: 1000000 INFO @ Wed, 08 Dec 2021 18:16:17: 10000000 INFO @ Wed, 08 Dec 2021 18:16:19: 6000000 INFO @ Wed, 08 Dec 2021 18:16:19: 2000000 INFO @ Wed, 08 Dec 2021 18:16:25: 11000000 INFO @ Wed, 08 Dec 2021 18:16:26: 7000000 INFO @ Wed, 08 Dec 2021 18:16:26: 3000000 INFO @ Wed, 08 Dec 2021 18:16:32: 12000000 INFO @ Wed, 08 Dec 2021 18:16:34: 8000000 INFO @ Wed, 08 Dec 2021 18:16:34: 4000000 INFO @ Wed, 08 Dec 2021 18:16:40: 13000000 INFO @ Wed, 08 Dec 2021 18:16:41: 9000000 INFO @ Wed, 08 Dec 2021 18:16:42: 5000000 INFO @ Wed, 08 Dec 2021 18:16:48: 14000000 INFO @ Wed, 08 Dec 2021 18:16:49: 10000000 INFO @ Wed, 08 Dec 2021 18:16:49: 6000000 INFO @ Wed, 08 Dec 2021 18:16:55: 15000000 INFO @ Wed, 08 Dec 2021 18:16:56: 11000000 INFO @ Wed, 08 Dec 2021 18:16:57: 7000000 INFO @ Wed, 08 Dec 2021 18:17:02: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:17:02: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:17:02: #1 total tags in treatment: 5925794 INFO @ Wed, 08 Dec 2021 18:17:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:17:02: #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 18:17:02: #1 tags after filtering in treatment: 4466657 INFO @ Wed, 08 Dec 2021 18:17:02: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 18:17:02: #1 finished! INFO @ Wed, 08 Dec 2021 18:17:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:17:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:17:02: #2 number of paired peaks: 1413 INFO @ Wed, 08 Dec 2021 18:17:02: start model_add_line... INFO @ Wed, 08 Dec 2021 18:17:02: start X-correlation... INFO @ Wed, 08 Dec 2021 18:17:02: end of X-cor INFO @ Wed, 08 Dec 2021 18:17:02: #2 finished! INFO @ Wed, 08 Dec 2021 18:17:02: #2 predicted fragment length is 267 bps INFO @ Wed, 08 Dec 2021 18:17:02: #2 alternative fragment length(s) may be 267 bps INFO @ Wed, 08 Dec 2021 18:17:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.05_model.r WARNING @ Wed, 08 Dec 2021 18:17:02: #2 Since the d (267) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:17:02: #2 You may need to consider one of the other alternative d(s): 267 WARNING @ Wed, 08 Dec 2021 18:17:02: #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 18:17:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:17:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:17:04: 12000000 INFO @ Wed, 08 Dec 2021 18:17:05: 8000000 INFO @ Wed, 08 Dec 2021 18:17:12: 13000000 INFO @ Wed, 08 Dec 2021 18:17:12: 9000000 INFO @ Wed, 08 Dec 2021 18:17:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:17:20: 10000000 INFO @ Wed, 08 Dec 2021 18:17:20: 14000000 INFO @ Wed, 08 Dec 2021 18:17:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:17:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:17:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.05_summits.bed INFO @ Wed, 08 Dec 2021 18:17:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2413 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:17:27: 11000000 INFO @ Wed, 08 Dec 2021 18:17:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:17:34: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:17:34: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:17:34: #1 total tags in treatment: 5925794 INFO @ Wed, 08 Dec 2021 18:17:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:17:34: #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 18:17:34: #1 tags after filtering in treatment: 4466657 INFO @ Wed, 08 Dec 2021 18:17:34: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 18:17:34: #1 finished! INFO @ Wed, 08 Dec 2021 18:17:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:17:34: #2 number of paired peaks: 1413 INFO @ Wed, 08 Dec 2021 18:17:34: start model_add_line... INFO @ Wed, 08 Dec 2021 18:17:34: start X-correlation... INFO @ Wed, 08 Dec 2021 18:17:34: end of X-cor INFO @ Wed, 08 Dec 2021 18:17:34: #2 finished! INFO @ Wed, 08 Dec 2021 18:17:34: #2 predicted fragment length is 267 bps INFO @ Wed, 08 Dec 2021 18:17:34: #2 alternative fragment length(s) may be 267 bps INFO @ Wed, 08 Dec 2021 18:17:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.10_model.r WARNING @ Wed, 08 Dec 2021 18:17:34: #2 Since the d (267) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:17:34: #2 You may need to consider one of the other alternative d(s): 267 WARNING @ Wed, 08 Dec 2021 18:17:34: #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 18:17:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:17:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:17:35: 12000000 INFO @ Wed, 08 Dec 2021 18:17:43: 13000000 INFO @ Wed, 08 Dec 2021 18:17:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:17:50: 14000000 INFO @ Wed, 08 Dec 2021 18:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.10_summits.bed INFO @ Wed, 08 Dec 2021 18:17:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:17:58: 15000000 INFO @ Wed, 08 Dec 2021 18:18:04: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:18:04: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:18:04: #1 total tags in treatment: 5925794 INFO @ Wed, 08 Dec 2021 18:18:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:18:04: #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 18:18:04: #1 tags after filtering in treatment: 4466657 INFO @ Wed, 08 Dec 2021 18:18:04: #1 Redundant rate of treatment: 0.25 INFO @ Wed, 08 Dec 2021 18:18:04: #1 finished! INFO @ Wed, 08 Dec 2021 18:18:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:18:05: #2 number of paired peaks: 1413 INFO @ Wed, 08 Dec 2021 18:18:05: start model_add_line... INFO @ Wed, 08 Dec 2021 18:18:05: start X-correlation... INFO @ Wed, 08 Dec 2021 18:18:05: end of X-cor INFO @ Wed, 08 Dec 2021 18:18:05: #2 finished! INFO @ Wed, 08 Dec 2021 18:18:05: #2 predicted fragment length is 267 bps INFO @ Wed, 08 Dec 2021 18:18:05: #2 alternative fragment length(s) may be 267 bps INFO @ Wed, 08 Dec 2021 18:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.20_model.r WARNING @ Wed, 08 Dec 2021 18:18:05: #2 Since the d (267) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:18:05: #2 You may need to consider one of the other alternative d(s): 267 WARNING @ Wed, 08 Dec 2021 18:18:05: #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 18:18:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:18:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:18:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:18:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:18:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641192/SRX10641192.20_summits.bed INFO @ Wed, 08 Dec 2021 18:18:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (741 records, 4 fields): 2 millis CompletedMACS2peakCalling