Job ID = 14159431 SRX = SRX8976691 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16049738 spots for SRR12483295/SRR12483295.sra Written 16049738 spots for SRR12483295/SRR12483295.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159636 ("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: 00:13:28 16049738 reads; of these: 16049738 (100.00%) were paired; of these: 1888520 (11.77%) aligned concordantly 0 times 11404555 (71.06%) aligned concordantly exactly 1 time 2756663 (17.18%) aligned concordantly >1 times ---- 1888520 pairs aligned concordantly 0 times; of these: 1190065 (63.02%) aligned discordantly 1 time ---- 698455 pairs aligned 0 times concordantly or discordantly; of these: 1396910 mates make up the pairs; of these: 472982 (33.86%) aligned 0 times 323802 (23.18%) aligned exactly 1 time 600126 (42.96%) aligned >1 times 98.53% overall alignment rate Time searching: 00:13:28 Overall time: 00:13:28 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] 1285550 / 15339047 = 0.0838 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 22:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.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 22:06:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:06:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:06:58: 1000000 INFO @ Wed, 08 Dec 2021 22:07:02: 2000000 INFO @ Wed, 08 Dec 2021 22:07:07: 3000000 INFO @ Wed, 08 Dec 2021 22:07:12: 4000000 INFO @ Wed, 08 Dec 2021 22:07:17: 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 @ Wed, 08 Dec 2021 22:07:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.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 22:07:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:07:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:07:22: 6000000 INFO @ Wed, 08 Dec 2021 22:07:25: 1000000 INFO @ Wed, 08 Dec 2021 22:07:27: 7000000 INFO @ Wed, 08 Dec 2021 22:07:30: 2000000 INFO @ Wed, 08 Dec 2021 22:07:33: 8000000 INFO @ Wed, 08 Dec 2021 22:07:35: 3000000 INFO @ Wed, 08 Dec 2021 22:07:37: 9000000 INFO @ Wed, 08 Dec 2021 22:07:40: 4000000 INFO @ Wed, 08 Dec 2021 22:07:42: 10000000 INFO @ Wed, 08 Dec 2021 22:07:46: 5000000 INFO @ Wed, 08 Dec 2021 22:07:46: 11000000 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 22:07:51: 6000000 INFO @ Wed, 08 Dec 2021 22:07:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.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 22:07:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:07:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:07:51: 12000000 INFO @ Wed, 08 Dec 2021 22:07:56: 13000000 INFO @ Wed, 08 Dec 2021 22:07:56: 7000000 INFO @ Wed, 08 Dec 2021 22:07:56: 1000000 INFO @ Wed, 08 Dec 2021 22:08:00: 14000000 INFO @ Wed, 08 Dec 2021 22:08:01: 8000000 INFO @ Wed, 08 Dec 2021 22:08:01: 2000000 INFO @ Wed, 08 Dec 2021 22:08:05: 15000000 INFO @ Wed, 08 Dec 2021 22:08:06: 9000000 INFO @ Wed, 08 Dec 2021 22:08:07: 3000000 INFO @ Wed, 08 Dec 2021 22:08:10: 16000000 INFO @ Wed, 08 Dec 2021 22:08:10: 10000000 INFO @ Wed, 08 Dec 2021 22:08:12: 4000000 INFO @ Wed, 08 Dec 2021 22:08:14: 17000000 INFO @ Wed, 08 Dec 2021 22:08:15: 11000000 INFO @ Wed, 08 Dec 2021 22:08:17: 5000000 INFO @ Wed, 08 Dec 2021 22:08:19: 18000000 INFO @ Wed, 08 Dec 2021 22:08:19: 12000000 INFO @ Wed, 08 Dec 2021 22:08:22: 6000000 INFO @ Wed, 08 Dec 2021 22:08:24: 19000000 INFO @ Wed, 08 Dec 2021 22:08:24: 13000000 INFO @ Wed, 08 Dec 2021 22:08:28: 7000000 INFO @ Wed, 08 Dec 2021 22:08:28: 20000000 INFO @ Wed, 08 Dec 2021 22:08:29: 14000000 INFO @ Wed, 08 Dec 2021 22:08:33: 21000000 INFO @ Wed, 08 Dec 2021 22:08:33: 8000000 INFO @ Wed, 08 Dec 2021 22:08:33: 15000000 INFO @ Wed, 08 Dec 2021 22:08:37: 22000000 INFO @ Wed, 08 Dec 2021 22:08:38: 9000000 INFO @ Wed, 08 Dec 2021 22:08:38: 16000000 INFO @ Wed, 08 Dec 2021 22:08:42: 23000000 INFO @ Wed, 08 Dec 2021 22:08:42: 10000000 INFO @ Wed, 08 Dec 2021 22:08:43: 17000000 INFO @ Wed, 08 Dec 2021 22:08:47: 24000000 INFO @ Wed, 08 Dec 2021 22:08:47: 11000000 INFO @ Wed, 08 Dec 2021 22:08:47: 18000000 INFO @ Wed, 08 Dec 2021 22:08:51: 25000000 INFO @ Wed, 08 Dec 2021 22:08:52: 12000000 INFO @ Wed, 08 Dec 2021 22:08:52: 19000000 INFO @ Wed, 08 Dec 2021 22:08:56: 26000000 INFO @ Wed, 08 Dec 2021 22:08:56: 13000000 INFO @ Wed, 08 Dec 2021 22:08:56: 20000000 INFO @ Wed, 08 Dec 2021 22:09:00: 27000000 INFO @ Wed, 08 Dec 2021 22:09:01: 21000000 INFO @ Wed, 08 Dec 2021 22:09:01: 14000000 INFO @ Wed, 08 Dec 2021 22:09:05: 28000000 INFO @ Wed, 08 Dec 2021 22:09:06: 22000000 INFO @ Wed, 08 Dec 2021 22:09:06: 15000000 INFO @ Wed, 08 Dec 2021 22:09:10: 29000000 INFO @ Wed, 08 Dec 2021 22:09:10: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:09:10: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:09:10: #1 total tags in treatment: 12949606 INFO @ Wed, 08 Dec 2021 22:09:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:09:10: #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 22:09:10: 23000000 INFO @ Wed, 08 Dec 2021 22:09:10: #1 tags after filtering in treatment: 11427621 INFO @ Wed, 08 Dec 2021 22:09:10: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 08 Dec 2021 22:09:10: #1 finished! INFO @ Wed, 08 Dec 2021 22:09:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:09:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:09:10: 16000000 INFO @ Wed, 08 Dec 2021 22:09:11: #2 number of paired peaks: 609 WARNING @ Wed, 08 Dec 2021 22:09:11: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Wed, 08 Dec 2021 22:09:11: start model_add_line... INFO @ Wed, 08 Dec 2021 22:09:11: start X-correlation... INFO @ Wed, 08 Dec 2021 22:09:11: end of X-cor INFO @ Wed, 08 Dec 2021 22:09:11: #2 finished! INFO @ Wed, 08 Dec 2021 22:09:11: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 22:09:11: #2 alternative fragment length(s) may be 3,142 bps INFO @ Wed, 08 Dec 2021 22:09:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.05_model.r INFO @ Wed, 08 Dec 2021 22:09:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:09:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:09:14: 24000000 INFO @ Wed, 08 Dec 2021 22:09:15: 17000000 INFO @ Wed, 08 Dec 2021 22:09:19: 25000000 INFO @ Wed, 08 Dec 2021 22:09:19: 18000000 INFO @ Wed, 08 Dec 2021 22:09:24: 26000000 INFO @ Wed, 08 Dec 2021 22:09:24: 19000000 INFO @ Wed, 08 Dec 2021 22:09:28: 27000000 INFO @ Wed, 08 Dec 2021 22:09:28: 20000000 INFO @ Wed, 08 Dec 2021 22:09:33: 28000000 INFO @ Wed, 08 Dec 2021 22:09:33: 21000000 INFO @ Wed, 08 Dec 2021 22:09:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 22:09:37: 29000000 INFO @ Wed, 08 Dec 2021 22:09:37: 22000000 INFO @ Wed, 08 Dec 2021 22:09:37: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:09:37: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:09:37: #1 total tags in treatment: 12949606 INFO @ Wed, 08 Dec 2021 22:09:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:09:37: #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 22:09:38: #1 tags after filtering in treatment: 11427621 INFO @ Wed, 08 Dec 2021 22:09:38: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 08 Dec 2021 22:09:38: #1 finished! INFO @ Wed, 08 Dec 2021 22:09:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:09:38: #2 looking for paired plus/minus strand peaks... BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:09:38: #2 number of paired peaks: 609 WARNING @ Wed, 08 Dec 2021 22:09:38: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Wed, 08 Dec 2021 22:09:38: start model_add_line... INFO @ Wed, 08 Dec 2021 22:09:38: start X-correlation... INFO @ Wed, 08 Dec 2021 22:09:39: end of X-cor INFO @ Wed, 08 Dec 2021 22:09:39: #2 finished! INFO @ Wed, 08 Dec 2021 22:09:39: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 22:09:39: #2 alternative fragment length(s) may be 3,142 bps INFO @ Wed, 08 Dec 2021 22:09:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.10_model.r INFO @ Wed, 08 Dec 2021 22:09:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:09:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:09:42: 23000000 INFO @ Wed, 08 Dec 2021 22:09:46: 24000000 INFO @ Wed, 08 Dec 2021 22:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.05_summits.bed INFO @ Wed, 08 Dec 2021 22:09:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:09:50: 25000000 INFO @ Wed, 08 Dec 2021 22:09:54: 26000000 INFO @ Wed, 08 Dec 2021 22:09:58: 27000000 INFO @ Wed, 08 Dec 2021 22:10:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:10:03: 28000000 INFO @ Wed, 08 Dec 2021 22:10:07: 29000000 INFO @ Wed, 08 Dec 2021 22:10:07: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:10:07: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:10:07: #1 total tags in treatment: 12949606 INFO @ Wed, 08 Dec 2021 22:10:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:10:07: #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 22:10:07: #1 tags after filtering in treatment: 11427621 INFO @ Wed, 08 Dec 2021 22:10:07: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 08 Dec 2021 22:10:07: #1 finished! INFO @ Wed, 08 Dec 2021 22:10:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:10:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:10:08: #2 number of paired peaks: 609 WARNING @ Wed, 08 Dec 2021 22:10:08: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Wed, 08 Dec 2021 22:10:08: start model_add_line... INFO @ Wed, 08 Dec 2021 22:10:08: start X-correlation... INFO @ Wed, 08 Dec 2021 22:10:08: end of X-cor INFO @ Wed, 08 Dec 2021 22:10:08: #2 finished! INFO @ Wed, 08 Dec 2021 22:10:08: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 22:10:08: #2 alternative fragment length(s) may be 3,142 bps INFO @ Wed, 08 Dec 2021 22:10:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.20_model.r INFO @ Wed, 08 Dec 2021 22:10:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:10:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.10_summits.bed INFO @ Wed, 08 Dec 2021 22:10:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:10:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:10:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:10:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:10:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976691/SRX8976691.20_summits.bed INFO @ Wed, 08 Dec 2021 22:10:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling