Job ID = 14159092 SRX = SRX8976738 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16731716 spots for SRR12483282/SRR12483282.sra Written 16731716 spots for SRR12483282/SRR12483282.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159355 ("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: 00:12:22 16731716 reads; of these: 16731716 (100.00%) were paired; of these: 389482 (2.33%) aligned concordantly 0 times 14245646 (85.14%) aligned concordantly exactly 1 time 2096588 (12.53%) aligned concordantly >1 times ---- 389482 pairs aligned concordantly 0 times; of these: 148906 (38.23%) aligned discordantly 1 time ---- 240576 pairs aligned 0 times concordantly or discordantly; of these: 481152 mates make up the pairs; of these: 253678 (52.72%) aligned 0 times 149051 (30.98%) aligned exactly 1 time 78423 (16.30%) aligned >1 times 99.24% overall alignment rate Time searching: 00:12:22 Overall time: 00:12:22 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] 521093 / 16445609 = 0.0317 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 19:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.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 19:35:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:35:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:35:35: 1000000 INFO @ Wed, 08 Dec 2021 19:35:40: 2000000 INFO @ Wed, 08 Dec 2021 19:35:45: 3000000 INFO @ Wed, 08 Dec 2021 19:35:50: 4000000 INFO @ Wed, 08 Dec 2021 19:35:54: 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 19:35:59: 6000000 INFO @ Wed, 08 Dec 2021 19:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.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 19:36:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:36:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:36:04: 7000000 INFO @ Wed, 08 Dec 2021 19:36:06: 1000000 INFO @ Wed, 08 Dec 2021 19:36:10: 8000000 INFO @ Wed, 08 Dec 2021 19:36:12: 2000000 INFO @ Wed, 08 Dec 2021 19:36:15: 9000000 INFO @ Wed, 08 Dec 2021 19:36:17: 3000000 INFO @ Wed, 08 Dec 2021 19:36:21: 10000000 INFO @ Wed, 08 Dec 2021 19:36:22: 4000000 INFO @ Wed, 08 Dec 2021 19:36:26: 11000000 INFO @ Wed, 08 Dec 2021 19:36:28: 5000000 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 19:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.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 19:36:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:36:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:36:31: 12000000 INFO @ Wed, 08 Dec 2021 19:36:33: 6000000 INFO @ Wed, 08 Dec 2021 19:36:36: 1000000 INFO @ Wed, 08 Dec 2021 19:36:37: 13000000 INFO @ Wed, 08 Dec 2021 19:36:39: 7000000 INFO @ Wed, 08 Dec 2021 19:36:42: 2000000 INFO @ Wed, 08 Dec 2021 19:36:42: 14000000 INFO @ Wed, 08 Dec 2021 19:36:44: 8000000 INFO @ Wed, 08 Dec 2021 19:36:47: 3000000 INFO @ Wed, 08 Dec 2021 19:36:47: 15000000 INFO @ Wed, 08 Dec 2021 19:36:50: 9000000 INFO @ Wed, 08 Dec 2021 19:36:53: 16000000 INFO @ Wed, 08 Dec 2021 19:36:53: 4000000 INFO @ Wed, 08 Dec 2021 19:36:55: 10000000 INFO @ Wed, 08 Dec 2021 19:36:58: 5000000 INFO @ Wed, 08 Dec 2021 19:36:58: 17000000 INFO @ Wed, 08 Dec 2021 19:37:01: 11000000 INFO @ Wed, 08 Dec 2021 19:37:03: 18000000 INFO @ Wed, 08 Dec 2021 19:37:04: 6000000 INFO @ Wed, 08 Dec 2021 19:37:06: 12000000 INFO @ Wed, 08 Dec 2021 19:37:09: 19000000 INFO @ Wed, 08 Dec 2021 19:37:09: 7000000 INFO @ Wed, 08 Dec 2021 19:37:11: 13000000 INFO @ Wed, 08 Dec 2021 19:37:14: 20000000 INFO @ Wed, 08 Dec 2021 19:37:15: 8000000 INFO @ Wed, 08 Dec 2021 19:37:17: 14000000 INFO @ Wed, 08 Dec 2021 19:37:20: 21000000 INFO @ Wed, 08 Dec 2021 19:37:20: 9000000 INFO @ Wed, 08 Dec 2021 19:37:22: 15000000 INFO @ Wed, 08 Dec 2021 19:37:25: 22000000 INFO @ Wed, 08 Dec 2021 19:37:26: 10000000 INFO @ Wed, 08 Dec 2021 19:37:28: 16000000 INFO @ Wed, 08 Dec 2021 19:37:30: 23000000 INFO @ Wed, 08 Dec 2021 19:37:31: 11000000 INFO @ Wed, 08 Dec 2021 19:37:33: 17000000 INFO @ Wed, 08 Dec 2021 19:37:35: 24000000 INFO @ Wed, 08 Dec 2021 19:37:37: 12000000 INFO @ Wed, 08 Dec 2021 19:37:38: 18000000 INFO @ Wed, 08 Dec 2021 19:37:41: 25000000 INFO @ Wed, 08 Dec 2021 19:37:42: 13000000 INFO @ Wed, 08 Dec 2021 19:37:44: 19000000 INFO @ Wed, 08 Dec 2021 19:37:46: 26000000 INFO @ Wed, 08 Dec 2021 19:37:47: 14000000 INFO @ Wed, 08 Dec 2021 19:37:49: 20000000 INFO @ Wed, 08 Dec 2021 19:37:51: 27000000 INFO @ Wed, 08 Dec 2021 19:37:53: 15000000 INFO @ Wed, 08 Dec 2021 19:37:55: 21000000 INFO @ Wed, 08 Dec 2021 19:37:56: 28000000 INFO @ Wed, 08 Dec 2021 19:37:58: 16000000 INFO @ Wed, 08 Dec 2021 19:38:00: 22000000 INFO @ Wed, 08 Dec 2021 19:38:01: 29000000 INFO @ Wed, 08 Dec 2021 19:38:04: 17000000 INFO @ Wed, 08 Dec 2021 19:38:05: 23000000 INFO @ Wed, 08 Dec 2021 19:38:06: 30000000 INFO @ Wed, 08 Dec 2021 19:38:09: 18000000 INFO @ Wed, 08 Dec 2021 19:38:11: 24000000 INFO @ Wed, 08 Dec 2021 19:38:12: 31000000 INFO @ Wed, 08 Dec 2021 19:38:14: 19000000 INFO @ Wed, 08 Dec 2021 19:38:16: 25000000 INFO @ Wed, 08 Dec 2021 19:38:17: 32000000 INFO @ Wed, 08 Dec 2021 19:38:18: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:38:18: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:38:18: #1 total tags in treatment: 15823635 INFO @ Wed, 08 Dec 2021 19:38:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:38:18: #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 19:38:18: #1 tags after filtering in treatment: 14563859 INFO @ Wed, 08 Dec 2021 19:38:18: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:38:18: #1 finished! INFO @ Wed, 08 Dec 2021 19:38:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:38:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:38:19: #2 number of paired peaks: 284 WARNING @ Wed, 08 Dec 2021 19:38:19: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Wed, 08 Dec 2021 19:38:19: start model_add_line... INFO @ Wed, 08 Dec 2021 19:38:19: start X-correlation... INFO @ Wed, 08 Dec 2021 19:38:19: end of X-cor INFO @ Wed, 08 Dec 2021 19:38:19: #2 finished! INFO @ Wed, 08 Dec 2021 19:38:19: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 19:38:19: #2 alternative fragment length(s) may be 4,136 bps INFO @ Wed, 08 Dec 2021 19:38:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.05_model.r INFO @ Wed, 08 Dec 2021 19:38:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:38:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:38:20: 20000000 INFO @ Wed, 08 Dec 2021 19:38:21: 26000000 INFO @ Wed, 08 Dec 2021 19:38:26: 21000000 INFO @ Wed, 08 Dec 2021 19:38:26: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:38:31: 22000000 INFO @ Wed, 08 Dec 2021 19:38:31: 28000000 INFO @ Wed, 08 Dec 2021 19:38:36: 23000000 INFO @ Wed, 08 Dec 2021 19:38:37: 29000000 INFO @ Wed, 08 Dec 2021 19:38:42: 24000000 INFO @ Wed, 08 Dec 2021 19:38:42: 30000000 INFO @ Wed, 08 Dec 2021 19:38:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:38:47: 25000000 INFO @ Wed, 08 Dec 2021 19:38:47: 31000000 INFO @ Wed, 08 Dec 2021 19:38:53: 32000000 INFO @ Wed, 08 Dec 2021 19:38:53: 26000000 INFO @ Wed, 08 Dec 2021 19:38:54: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:38:54: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:38:54: #1 total tags in treatment: 15823635 INFO @ Wed, 08 Dec 2021 19:38:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:38:54: #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 19:38:54: #1 tags after filtering in treatment: 14563859 INFO @ Wed, 08 Dec 2021 19:38:54: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:38:54: #1 finished! INFO @ Wed, 08 Dec 2021 19:38:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:38:55: #2 number of paired peaks: 284 WARNING @ Wed, 08 Dec 2021 19:38:55: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Wed, 08 Dec 2021 19:38:55: start model_add_line... INFO @ Wed, 08 Dec 2021 19:38:55: start X-correlation... INFO @ Wed, 08 Dec 2021 19:38:55: end of X-cor INFO @ Wed, 08 Dec 2021 19:38:55: #2 finished! INFO @ Wed, 08 Dec 2021 19:38:55: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 19:38:55: #2 alternative fragment length(s) may be 4,136 bps INFO @ Wed, 08 Dec 2021 19:38:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.10_model.r INFO @ Wed, 08 Dec 2021 19:38:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:38:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:38:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:38:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:38:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.05_summits.bed INFO @ Wed, 08 Dec 2021 19:38:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (349 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:38:58: 27000000 INFO @ Wed, 08 Dec 2021 19:39:02: 28000000 INFO @ Wed, 08 Dec 2021 19:39:07: 29000000 INFO @ Wed, 08 Dec 2021 19:39:12: 30000000 INFO @ Wed, 08 Dec 2021 19:39:16: 31000000 INFO @ Wed, 08 Dec 2021 19:39:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:39:21: 32000000 INFO @ Wed, 08 Dec 2021 19:39:22: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:39:22: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:39:22: #1 total tags in treatment: 15823635 INFO @ Wed, 08 Dec 2021 19:39:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:39:22: #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 19:39:22: #1 tags after filtering in treatment: 14563859 INFO @ Wed, 08 Dec 2021 19:39:22: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:39:22: #1 finished! INFO @ Wed, 08 Dec 2021 19:39:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:39:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:39:23: #2 number of paired peaks: 284 WARNING @ Wed, 08 Dec 2021 19:39:23: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Wed, 08 Dec 2021 19:39:23: start model_add_line... INFO @ Wed, 08 Dec 2021 19:39:23: start X-correlation... INFO @ Wed, 08 Dec 2021 19:39:23: end of X-cor INFO @ Wed, 08 Dec 2021 19:39:23: #2 finished! INFO @ Wed, 08 Dec 2021 19:39:23: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 19:39:23: #2 alternative fragment length(s) may be 4,136 bps INFO @ Wed, 08 Dec 2021 19:39:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.20_model.r INFO @ Wed, 08 Dec 2021 19:39:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:39:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:39:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:39:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:39:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.10_summits.bed INFO @ Wed, 08 Dec 2021 19:39:32: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (250 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:39:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:40:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:40:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976738/SRX8976738.20_summits.bed INFO @ Wed, 08 Dec 2021 19:40:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling