Job ID = 14158321 SRX = SRX10342593 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10454745 spots for SRR13964642/SRR13964642.sra Written 10454745 spots for SRR13964642/SRR13964642.sra Read 11513588 spots for SRR13964643/SRR13964643.sra Written 11513588 spots for SRR13964643/SRR13964643.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158881 ("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: 00:15:00 21968333 reads; of these: 21968333 (100.00%) were paired; of these: 5845001 (26.61%) aligned concordantly 0 times 14267644 (64.95%) aligned concordantly exactly 1 time 1855688 (8.45%) aligned concordantly >1 times ---- 5845001 pairs aligned concordantly 0 times; of these: 4317272 (73.86%) aligned discordantly 1 time ---- 1527729 pairs aligned 0 times concordantly or discordantly; of these: 3055458 mates make up the pairs; of these: 1426170 (46.68%) aligned 0 times 661206 (21.64%) aligned exactly 1 time 968082 (31.68%) aligned >1 times 96.75% overall alignment rate Time searching: 00:15:00 Overall time: 00:15:00 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] 3142477 / 20430685 = 0.1538 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 16:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.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 16:26:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:26:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:26:20: 1000000 INFO @ Wed, 08 Dec 2021 16:26:24: 2000000 INFO @ Wed, 08 Dec 2021 16:26:28: 3000000 INFO @ Wed, 08 Dec 2021 16:26:31: 4000000 INFO @ Wed, 08 Dec 2021 16:26:35: 5000000 INFO @ Wed, 08 Dec 2021 16:26:39: 6000000 INFO @ Wed, 08 Dec 2021 16:26:43: 7000000 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 16:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.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 16:26:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:26:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:26:47: 8000000 INFO @ Wed, 08 Dec 2021 16:26:50: 1000000 INFO @ Wed, 08 Dec 2021 16:26:51: 9000000 INFO @ Wed, 08 Dec 2021 16:26:54: 2000000 INFO @ Wed, 08 Dec 2021 16:26:54: 10000000 INFO @ Wed, 08 Dec 2021 16:26:58: 3000000 INFO @ Wed, 08 Dec 2021 16:26:58: 11000000 INFO @ Wed, 08 Dec 2021 16:27:01: 4000000 INFO @ Wed, 08 Dec 2021 16:27:02: 12000000 INFO @ Wed, 08 Dec 2021 16:27:05: 5000000 INFO @ Wed, 08 Dec 2021 16:27:06: 13000000 INFO @ Wed, 08 Dec 2021 16:27:09: 6000000 INFO @ Wed, 08 Dec 2021 16:27:10: 14000000 INFO @ Wed, 08 Dec 2021 16:27:13: 7000000 INFO @ Wed, 08 Dec 2021 16:27:14: 15000000 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 16:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.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 16:27:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:27:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:27:17: 8000000 INFO @ Wed, 08 Dec 2021 16:27:18: 16000000 INFO @ Wed, 08 Dec 2021 16:27:21: 1000000 INFO @ Wed, 08 Dec 2021 16:27:21: 9000000 INFO @ Wed, 08 Dec 2021 16:27:22: 17000000 INFO @ Wed, 08 Dec 2021 16:27:25: 10000000 INFO @ Wed, 08 Dec 2021 16:27:26: 2000000 INFO @ Wed, 08 Dec 2021 16:27:26: 18000000 INFO @ Wed, 08 Dec 2021 16:27:29: 11000000 INFO @ Wed, 08 Dec 2021 16:27:30: 19000000 INFO @ Wed, 08 Dec 2021 16:27:30: 3000000 INFO @ Wed, 08 Dec 2021 16:27:33: 12000000 INFO @ Wed, 08 Dec 2021 16:27:34: 20000000 INFO @ Wed, 08 Dec 2021 16:27:35: 4000000 INFO @ Wed, 08 Dec 2021 16:27:37: 13000000 INFO @ Wed, 08 Dec 2021 16:27:38: 21000000 INFO @ Wed, 08 Dec 2021 16:27:40: 5000000 INFO @ Wed, 08 Dec 2021 16:27:41: 14000000 INFO @ Wed, 08 Dec 2021 16:27:42: 22000000 INFO @ Wed, 08 Dec 2021 16:27:45: 6000000 INFO @ Wed, 08 Dec 2021 16:27:45: 15000000 INFO @ Wed, 08 Dec 2021 16:27:46: 23000000 INFO @ Wed, 08 Dec 2021 16:27:49: 16000000 INFO @ Wed, 08 Dec 2021 16:27:49: 7000000 INFO @ Wed, 08 Dec 2021 16:27:50: 24000000 INFO @ Wed, 08 Dec 2021 16:27:53: 17000000 INFO @ Wed, 08 Dec 2021 16:27:54: 25000000 INFO @ Wed, 08 Dec 2021 16:27:54: 8000000 INFO @ Wed, 08 Dec 2021 16:27:57: 18000000 INFO @ Wed, 08 Dec 2021 16:27:58: 26000000 INFO @ Wed, 08 Dec 2021 16:27:59: 9000000 INFO @ Wed, 08 Dec 2021 16:28:01: 19000000 INFO @ Wed, 08 Dec 2021 16:28:02: 27000000 INFO @ Wed, 08 Dec 2021 16:28:04: 10000000 INFO @ Wed, 08 Dec 2021 16:28:05: 20000000 INFO @ Wed, 08 Dec 2021 16:28:06: 28000000 INFO @ Wed, 08 Dec 2021 16:28:08: 11000000 INFO @ Wed, 08 Dec 2021 16:28:09: 21000000 INFO @ Wed, 08 Dec 2021 16:28:10: 29000000 INFO @ Wed, 08 Dec 2021 16:28:13: 22000000 INFO @ Wed, 08 Dec 2021 16:28:13: 12000000 INFO @ Wed, 08 Dec 2021 16:28:14: 30000000 INFO @ Wed, 08 Dec 2021 16:28:17: 23000000 INFO @ Wed, 08 Dec 2021 16:28:18: 31000000 INFO @ Wed, 08 Dec 2021 16:28:18: 13000000 INFO @ Wed, 08 Dec 2021 16:28:21: 24000000 INFO @ Wed, 08 Dec 2021 16:28:21: 32000000 INFO @ Wed, 08 Dec 2021 16:28:23: 14000000 INFO @ Wed, 08 Dec 2021 16:28:25: 25000000 INFO @ Wed, 08 Dec 2021 16:28:25: 33000000 INFO @ Wed, 08 Dec 2021 16:28:27: 15000000 INFO @ Wed, 08 Dec 2021 16:28:29: 26000000 INFO @ Wed, 08 Dec 2021 16:28:29: 34000000 INFO @ Wed, 08 Dec 2021 16:28:32: 16000000 INFO @ Wed, 08 Dec 2021 16:28:33: 27000000 INFO @ Wed, 08 Dec 2021 16:28:33: 35000000 INFO @ Wed, 08 Dec 2021 16:28:37: 28000000 INFO @ Wed, 08 Dec 2021 16:28:37: 17000000 INFO @ Wed, 08 Dec 2021 16:28:37: 36000000 INFO @ Wed, 08 Dec 2021 16:28:38: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:28:38: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:28:38: #1 total tags in treatment: 13480043 INFO @ Wed, 08 Dec 2021 16:28:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:28:38: #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 16:28:38: #1 tags after filtering in treatment: 12374912 INFO @ Wed, 08 Dec 2021 16:28:38: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:28:38: #1 finished! INFO @ Wed, 08 Dec 2021 16:28:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:28:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:28:39: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 16:28:39: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 16:28:39: start model_add_line... INFO @ Wed, 08 Dec 2021 16:28:39: start X-correlation... INFO @ Wed, 08 Dec 2021 16:28:39: end of X-cor INFO @ Wed, 08 Dec 2021 16:28:39: #2 finished! INFO @ Wed, 08 Dec 2021 16:28:39: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 16:28:39: #2 alternative fragment length(s) may be 4,139,157 bps INFO @ Wed, 08 Dec 2021 16:28:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.05_model.r INFO @ Wed, 08 Dec 2021 16:28:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:28:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:28:41: 29000000 INFO @ Wed, 08 Dec 2021 16:28:42: 18000000 INFO @ Wed, 08 Dec 2021 16:28:45: 30000000 INFO @ Wed, 08 Dec 2021 16:28:46: 19000000 INFO @ Wed, 08 Dec 2021 16:28:49: 31000000 INFO @ Wed, 08 Dec 2021 16:28:51: 20000000 INFO @ Wed, 08 Dec 2021 16:28:52: 32000000 INFO @ Wed, 08 Dec 2021 16:28:56: 21000000 INFO @ Wed, 08 Dec 2021 16:28:56: 33000000 INFO @ Wed, 08 Dec 2021 16:29:00: 34000000 INFO @ Wed, 08 Dec 2021 16:29:01: 22000000 INFO @ Wed, 08 Dec 2021 16:29:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:29:04: 35000000 INFO @ Wed, 08 Dec 2021 16:29:05: 23000000 INFO @ Wed, 08 Dec 2021 16:29:08: 36000000 INFO @ Wed, 08 Dec 2021 16:29:09: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:29:09: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:29:09: #1 total tags in treatment: 13480043 INFO @ Wed, 08 Dec 2021 16:29:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:29:09: #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 16:29:09: #1 tags after filtering in treatment: 12374912 INFO @ Wed, 08 Dec 2021 16:29:09: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:29:09: #1 finished! INFO @ Wed, 08 Dec 2021 16:29:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:29:10: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 16:29:10: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 16:29:10: start model_add_line... INFO @ Wed, 08 Dec 2021 16:29:10: start X-correlation... INFO @ Wed, 08 Dec 2021 16:29:10: end of X-cor INFO @ Wed, 08 Dec 2021 16:29:10: #2 finished! INFO @ Wed, 08 Dec 2021 16:29:10: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 16:29:10: #2 alternative fragment length(s) may be 4,139,157 bps INFO @ Wed, 08 Dec 2021 16:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.10_model.r INFO @ Wed, 08 Dec 2021 16:29:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:29:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:29:10: 24000000 INFO @ Wed, 08 Dec 2021 16:29:15: 25000000 INFO @ Wed, 08 Dec 2021 16:29:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:29:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:29:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.05_summits.bed INFO @ Wed, 08 Dec 2021 16:29:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4785 records, 4 fields): 200 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:29:19: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:29:24: 27000000 INFO @ Wed, 08 Dec 2021 16:29:29: 28000000 INFO @ Wed, 08 Dec 2021 16:29:33: 29000000 INFO @ Wed, 08 Dec 2021 16:29:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:29:38: 30000000 INFO @ Wed, 08 Dec 2021 16:29:42: 31000000 INFO @ Wed, 08 Dec 2021 16:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.10_summits.bed INFO @ Wed, 08 Dec 2021 16:29:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2655 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:29:47: 32000000 INFO @ Wed, 08 Dec 2021 16:29:51: 33000000 INFO @ Wed, 08 Dec 2021 16:29:55: 34000000 INFO @ Wed, 08 Dec 2021 16:30:00: 35000000 INFO @ Wed, 08 Dec 2021 16:30:04: 36000000 INFO @ Wed, 08 Dec 2021 16:30:05: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:30:05: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:30:05: #1 total tags in treatment: 13480043 INFO @ Wed, 08 Dec 2021 16:30:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:30:05: #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 16:30:05: #1 tags after filtering in treatment: 12374912 INFO @ Wed, 08 Dec 2021 16:30:05: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:30:05: #1 finished! INFO @ Wed, 08 Dec 2021 16:30:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:30:06: #2 number of paired peaks: 370 WARNING @ Wed, 08 Dec 2021 16:30:06: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Wed, 08 Dec 2021 16:30:06: start model_add_line... INFO @ Wed, 08 Dec 2021 16:30:06: start X-correlation... INFO @ Wed, 08 Dec 2021 16:30:06: end of X-cor INFO @ Wed, 08 Dec 2021 16:30:06: #2 finished! INFO @ Wed, 08 Dec 2021 16:30:06: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 16:30:06: #2 alternative fragment length(s) may be 4,139,157 bps INFO @ Wed, 08 Dec 2021 16:30:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.20_model.r INFO @ Wed, 08 Dec 2021 16:30:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:30:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:30:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342593/SRX10342593.20_summits.bed INFO @ Wed, 08 Dec 2021 16:30:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (444 records, 4 fields): 1 millis CompletedMACS2peakCalling