Job ID = 14158790 SRX = SRX8976709 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11138175 spots for SRR12483313/SRR12483313.sra Written 11138175 spots for SRR12483313/SRR12483313.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159207 ("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: 00:14:43 11138175 reads; of these: 11138175 (100.00%) were paired; of these: 2437050 (21.88%) aligned concordantly 0 times 7035743 (63.17%) aligned concordantly exactly 1 time 1665382 (14.95%) aligned concordantly >1 times ---- 2437050 pairs aligned concordantly 0 times; of these: 1652246 (67.80%) aligned discordantly 1 time ---- 784804 pairs aligned 0 times concordantly or discordantly; of these: 1569608 mates make up the pairs; of these: 571428 (36.41%) aligned 0 times 435899 (27.77%) aligned exactly 1 time 562281 (35.82%) aligned >1 times 97.43% overall alignment rate Time searching: 00:14:43 Overall time: 00:14:43 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] 409900 / 10347278 = 0.0396 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 18:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.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 18:15:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:15:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:15:46: 1000000 INFO @ Wed, 08 Dec 2021 18:15:52: 2000000 INFO @ Wed, 08 Dec 2021 18:15:57: 3000000 INFO @ Wed, 08 Dec 2021 18:16:03: 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 18:16:09: 5000000 INFO @ Wed, 08 Dec 2021 18:16:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.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 18:16:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:16:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:16:15: 6000000 INFO @ Wed, 08 Dec 2021 18:16:18: 1000000 INFO @ Wed, 08 Dec 2021 18:16:20: 7000000 INFO @ Wed, 08 Dec 2021 18:16:26: 2000000 INFO @ Wed, 08 Dec 2021 18:16:27: 8000000 INFO @ Wed, 08 Dec 2021 18:16:32: 9000000 INFO @ Wed, 08 Dec 2021 18:16:33: 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 18:16:38: 10000000 INFO @ Wed, 08 Dec 2021 18:16:40: 4000000 INFO @ Wed, 08 Dec 2021 18:16:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.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 18:16:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:16:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:16:44: 11000000 INFO @ Wed, 08 Dec 2021 18:16:46: 5000000 INFO @ Wed, 08 Dec 2021 18:16:47: 1000000 INFO @ Wed, 08 Dec 2021 18:16:49: 12000000 INFO @ Wed, 08 Dec 2021 18:16:53: 6000000 INFO @ Wed, 08 Dec 2021 18:16:54: 2000000 INFO @ Wed, 08 Dec 2021 18:16:56: 13000000 INFO @ Wed, 08 Dec 2021 18:17:00: 7000000 INFO @ Wed, 08 Dec 2021 18:17:02: 14000000 INFO @ Wed, 08 Dec 2021 18:17:02: 3000000 INFO @ Wed, 08 Dec 2021 18:17:07: 15000000 INFO @ Wed, 08 Dec 2021 18:17:07: 8000000 INFO @ Wed, 08 Dec 2021 18:17:09: 4000000 INFO @ Wed, 08 Dec 2021 18:17:12: 16000000 INFO @ Wed, 08 Dec 2021 18:17:14: 9000000 INFO @ Wed, 08 Dec 2021 18:17:17: 5000000 INFO @ Wed, 08 Dec 2021 18:17:18: 17000000 INFO @ Wed, 08 Dec 2021 18:17:21: 10000000 INFO @ Wed, 08 Dec 2021 18:17:24: 18000000 INFO @ Wed, 08 Dec 2021 18:17:24: 6000000 INFO @ Wed, 08 Dec 2021 18:17:28: 11000000 INFO @ Wed, 08 Dec 2021 18:17:30: 19000000 INFO @ Wed, 08 Dec 2021 18:17:32: 7000000 INFO @ Wed, 08 Dec 2021 18:17:35: 12000000 INFO @ Wed, 08 Dec 2021 18:17:36: 20000000 INFO @ Wed, 08 Dec 2021 18:17:39: 8000000 INFO @ Wed, 08 Dec 2021 18:17:41: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:17:41: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:17:41: #1 total tags in treatment: 8333049 INFO @ Wed, 08 Dec 2021 18:17:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:17:41: #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 18:17:41: #1 tags after filtering in treatment: 7624876 INFO @ Wed, 08 Dec 2021 18:17:41: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:17:41: #1 finished! INFO @ Wed, 08 Dec 2021 18:17:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:17:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:17:41: #2 number of paired peaks: 560 WARNING @ Wed, 08 Dec 2021 18:17:41: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Wed, 08 Dec 2021 18:17:41: start model_add_line... INFO @ Wed, 08 Dec 2021 18:17:41: start X-correlation... INFO @ Wed, 08 Dec 2021 18:17:41: end of X-cor INFO @ Wed, 08 Dec 2021 18:17:41: #2 finished! INFO @ Wed, 08 Dec 2021 18:17:41: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 18:17:41: #2 alternative fragment length(s) may be 4,166 bps INFO @ Wed, 08 Dec 2021 18:17:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.05_model.r INFO @ Wed, 08 Dec 2021 18:17:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:17:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:17:42: 13000000 INFO @ Wed, 08 Dec 2021 18:17:47: 9000000 INFO @ Wed, 08 Dec 2021 18:17:50: 14000000 INFO @ Wed, 08 Dec 2021 18:17:54: 10000000 INFO @ Wed, 08 Dec 2021 18:17:57: 15000000 INFO @ Wed, 08 Dec 2021 18:17:59: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:18:02: 11000000 INFO @ Wed, 08 Dec 2021 18:18:05: 16000000 INFO @ Wed, 08 Dec 2021 18:18:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:18:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:18:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.05_summits.bed INFO @ Wed, 08 Dec 2021 18:18:08: Done! INFO @ Wed, 08 Dec 2021 18:18:09: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:18:13: 17000000 INFO @ Wed, 08 Dec 2021 18:18:15: 13000000 INFO @ Wed, 08 Dec 2021 18:18:21: 18000000 INFO @ Wed, 08 Dec 2021 18:18:23: 14000000 INFO @ Wed, 08 Dec 2021 18:18:29: 19000000 INFO @ Wed, 08 Dec 2021 18:18:30: 15000000 INFO @ Wed, 08 Dec 2021 18:18:37: 20000000 INFO @ Wed, 08 Dec 2021 18:18:38: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:18:44: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:18:44: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:18:44: #1 total tags in treatment: 8333049 INFO @ Wed, 08 Dec 2021 18:18:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:18:44: #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 18:18:44: #1 tags after filtering in treatment: 7624876 INFO @ Wed, 08 Dec 2021 18:18:44: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:18:44: #1 finished! INFO @ Wed, 08 Dec 2021 18:18:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:18:44: #2 number of paired peaks: 560 WARNING @ Wed, 08 Dec 2021 18:18:44: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Wed, 08 Dec 2021 18:18:44: start model_add_line... INFO @ Wed, 08 Dec 2021 18:18:45: start X-correlation... INFO @ Wed, 08 Dec 2021 18:18:45: end of X-cor INFO @ Wed, 08 Dec 2021 18:18:45: #2 finished! INFO @ Wed, 08 Dec 2021 18:18:45: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 18:18:45: #2 alternative fragment length(s) may be 4,166 bps INFO @ Wed, 08 Dec 2021 18:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.10_model.r INFO @ Wed, 08 Dec 2021 18:18:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:18:46: 17000000 INFO @ Wed, 08 Dec 2021 18:18:54: 18000000 INFO @ Wed, 08 Dec 2021 18:19:02: 19000000 INFO @ Wed, 08 Dec 2021 18:19:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:19:10: 20000000 INFO @ Wed, 08 Dec 2021 18:19:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:19:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:19:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.10_summits.bed INFO @ Wed, 08 Dec 2021 18:19:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (336 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:19:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:19:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:19:17: #1 total tags in treatment: 8333049 INFO @ Wed, 08 Dec 2021 18:19:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:19:17: #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 18:19:17: #1 tags after filtering in treatment: 7624876 INFO @ Wed, 08 Dec 2021 18:19:17: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:19:17: #1 finished! INFO @ Wed, 08 Dec 2021 18:19:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:19:17: #2 number of paired peaks: 560 WARNING @ Wed, 08 Dec 2021 18:19:17: Fewer paired peaks (560) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 560 pairs to build model! INFO @ Wed, 08 Dec 2021 18:19:17: start model_add_line... INFO @ Wed, 08 Dec 2021 18:19:18: start X-correlation... INFO @ Wed, 08 Dec 2021 18:19:18: end of X-cor INFO @ Wed, 08 Dec 2021 18:19:18: #2 finished! INFO @ Wed, 08 Dec 2021 18:19:18: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 18:19:18: #2 alternative fragment length(s) may be 4,166 bps INFO @ Wed, 08 Dec 2021 18:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.20_model.r INFO @ Wed, 08 Dec 2021 18:19:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:19:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:19:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:19:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:19:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976709/SRX8976709.20_summits.bed INFO @ Wed, 08 Dec 2021 18:19:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (223 records, 4 fields): 2 millis CompletedMACS2peakCalling