Job ID = 14159093 SRX = SRX8976739 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15492033 spots for SRR12483283/SRR12483283.sra Written 15492033 spots for SRR12483283/SRR12483283.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159357 ("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: 00:12:16 15492033 reads; of these: 15492033 (100.00%) were paired; of these: 1326432 (8.56%) aligned concordantly 0 times 12308782 (79.45%) aligned concordantly exactly 1 time 1856819 (11.99%) aligned concordantly >1 times ---- 1326432 pairs aligned concordantly 0 times; of these: 992248 (74.81%) aligned discordantly 1 time ---- 334184 pairs aligned 0 times concordantly or discordantly; of these: 668368 mates make up the pairs; of these: 185862 (27.81%) aligned 0 times 212353 (31.77%) aligned exactly 1 time 270153 (40.42%) aligned >1 times 99.40% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 473018 / 15123689 = 0.0313 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 19:35:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.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 19:35:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:35:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:35:28: 1000000 INFO @ Wed, 08 Dec 2021 19:35:32: 2000000 INFO @ Wed, 08 Dec 2021 19:35:37: 3000000 INFO @ Wed, 08 Dec 2021 19:35:42: 4000000 INFO @ Wed, 08 Dec 2021 19:35:46: 5000000 INFO @ Wed, 08 Dec 2021 19:35:51: 6000000 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 19:35:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.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 19:35:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:35:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:35:56: 7000000 INFO @ Wed, 08 Dec 2021 19:35:58: 1000000 INFO @ Wed, 08 Dec 2021 19:36:01: 8000000 INFO @ Wed, 08 Dec 2021 19:36:04: 2000000 INFO @ Wed, 08 Dec 2021 19:36:06: 9000000 INFO @ Wed, 08 Dec 2021 19:36:10: 3000000 INFO @ Wed, 08 Dec 2021 19:36:11: 10000000 INFO @ Wed, 08 Dec 2021 19:36:16: 4000000 INFO @ Wed, 08 Dec 2021 19:36:16: 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 19:36:22: 12000000 INFO @ Wed, 08 Dec 2021 19:36:22: 5000000 INFO @ Wed, 08 Dec 2021 19:36:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.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 19:36:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:36:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:36:27: 13000000 INFO @ Wed, 08 Dec 2021 19:36:27: 6000000 INFO @ Wed, 08 Dec 2021 19:36:29: 1000000 INFO @ Wed, 08 Dec 2021 19:36:32: 14000000 INFO @ Wed, 08 Dec 2021 19:36:33: 7000000 INFO @ Wed, 08 Dec 2021 19:36:35: 2000000 INFO @ Wed, 08 Dec 2021 19:36:37: 15000000 INFO @ Wed, 08 Dec 2021 19:36:39: 8000000 INFO @ Wed, 08 Dec 2021 19:36:41: 3000000 INFO @ Wed, 08 Dec 2021 19:36:43: 16000000 INFO @ Wed, 08 Dec 2021 19:36:45: 9000000 INFO @ Wed, 08 Dec 2021 19:36:47: 4000000 INFO @ Wed, 08 Dec 2021 19:36:48: 17000000 INFO @ Wed, 08 Dec 2021 19:36:52: 10000000 INFO @ Wed, 08 Dec 2021 19:36:53: 5000000 INFO @ Wed, 08 Dec 2021 19:36:53: 18000000 INFO @ Wed, 08 Dec 2021 19:36:58: 11000000 INFO @ Wed, 08 Dec 2021 19:36:58: 6000000 INFO @ Wed, 08 Dec 2021 19:36:59: 19000000 INFO @ Wed, 08 Dec 2021 19:37:04: 12000000 INFO @ Wed, 08 Dec 2021 19:37:04: 20000000 INFO @ Wed, 08 Dec 2021 19:37:04: 7000000 INFO @ Wed, 08 Dec 2021 19:37:09: 21000000 INFO @ Wed, 08 Dec 2021 19:37:10: 13000000 INFO @ Wed, 08 Dec 2021 19:37:10: 8000000 INFO @ Wed, 08 Dec 2021 19:37:15: 22000000 INFO @ Wed, 08 Dec 2021 19:37:16: 14000000 INFO @ Wed, 08 Dec 2021 19:37:16: 9000000 INFO @ Wed, 08 Dec 2021 19:37:20: 23000000 INFO @ Wed, 08 Dec 2021 19:37:22: 15000000 INFO @ Wed, 08 Dec 2021 19:37:22: 10000000 INFO @ Wed, 08 Dec 2021 19:37:25: 24000000 INFO @ Wed, 08 Dec 2021 19:37:28: 16000000 INFO @ Wed, 08 Dec 2021 19:37:28: 11000000 INFO @ Wed, 08 Dec 2021 19:37:30: 25000000 INFO @ Wed, 08 Dec 2021 19:37:34: 12000000 INFO @ Wed, 08 Dec 2021 19:37:34: 17000000 INFO @ Wed, 08 Dec 2021 19:37:36: 26000000 INFO @ Wed, 08 Dec 2021 19:37:40: 13000000 INFO @ Wed, 08 Dec 2021 19:37:40: 18000000 INFO @ Wed, 08 Dec 2021 19:37:41: 27000000 INFO @ Wed, 08 Dec 2021 19:37:45: 14000000 INFO @ Wed, 08 Dec 2021 19:37:46: 19000000 INFO @ Wed, 08 Dec 2021 19:37:46: 28000000 INFO @ Wed, 08 Dec 2021 19:37:51: 29000000 INFO @ Wed, 08 Dec 2021 19:37:51: 15000000 INFO @ Wed, 08 Dec 2021 19:37:52: 20000000 INFO @ Wed, 08 Dec 2021 19:37:56: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:37:56: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:37:56: #1 total tags in treatment: 13715814 INFO @ Wed, 08 Dec 2021 19:37:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:37:56: #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 19:37:56: #1 tags after filtering in treatment: 12701913 INFO @ Wed, 08 Dec 2021 19:37:56: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:37:56: #1 finished! INFO @ Wed, 08 Dec 2021 19:37:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:37:57: #2 number of paired peaks: 329 WARNING @ Wed, 08 Dec 2021 19:37:57: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Wed, 08 Dec 2021 19:37:57: start model_add_line... INFO @ Wed, 08 Dec 2021 19:37:57: start X-correlation... INFO @ Wed, 08 Dec 2021 19:37:57: end of X-cor INFO @ Wed, 08 Dec 2021 19:37:57: #2 finished! INFO @ Wed, 08 Dec 2021 19:37:57: #2 predicted fragment length is 133 bps INFO @ Wed, 08 Dec 2021 19:37:57: #2 alternative fragment length(s) may be 3,133,150,176 bps INFO @ Wed, 08 Dec 2021 19:37:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.05_model.r INFO @ Wed, 08 Dec 2021 19:37:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:37:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:37:57: 16000000 INFO @ Wed, 08 Dec 2021 19:37:58: 21000000 INFO @ Wed, 08 Dec 2021 19:38:03: 17000000 INFO @ Wed, 08 Dec 2021 19:38:04: 22000000 INFO @ Wed, 08 Dec 2021 19:38:09: 18000000 INFO @ Wed, 08 Dec 2021 19:38:10: 23000000 INFO @ Wed, 08 Dec 2021 19:38:14: 19000000 INFO @ Wed, 08 Dec 2021 19:38:16: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:38:20: 20000000 INFO @ Wed, 08 Dec 2021 19:38:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:38:22: 25000000 INFO @ Wed, 08 Dec 2021 19:38:26: 21000000 INFO @ Wed, 08 Dec 2021 19:38:28: 26000000 INFO @ Wed, 08 Dec 2021 19:38:31: 22000000 INFO @ Wed, 08 Dec 2021 19:38:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:38:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:38:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.05_summits.bed INFO @ Wed, 08 Dec 2021 19:38:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:38:34: 27000000 INFO @ Wed, 08 Dec 2021 19:38:37: 23000000 INFO @ Wed, 08 Dec 2021 19:38:39: 28000000 INFO @ Wed, 08 Dec 2021 19:38:43: 24000000 INFO @ Wed, 08 Dec 2021 19:38:45: 29000000 INFO @ Wed, 08 Dec 2021 19:38:49: 25000000 INFO @ Wed, 08 Dec 2021 19:38:50: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:38:50: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:38:50: #1 total tags in treatment: 13715814 INFO @ Wed, 08 Dec 2021 19:38:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:38:50: #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 19:38:51: #1 tags after filtering in treatment: 12701913 INFO @ Wed, 08 Dec 2021 19:38:51: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:38:51: #1 finished! INFO @ Wed, 08 Dec 2021 19:38:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:38:51: #2 number of paired peaks: 329 WARNING @ Wed, 08 Dec 2021 19:38:51: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Wed, 08 Dec 2021 19:38:51: start model_add_line... INFO @ Wed, 08 Dec 2021 19:38:51: start X-correlation... INFO @ Wed, 08 Dec 2021 19:38:52: end of X-cor INFO @ Wed, 08 Dec 2021 19:38:52: #2 finished! INFO @ Wed, 08 Dec 2021 19:38:52: #2 predicted fragment length is 133 bps INFO @ Wed, 08 Dec 2021 19:38:52: #2 alternative fragment length(s) may be 3,133,150,176 bps INFO @ Wed, 08 Dec 2021 19:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.10_model.r INFO @ Wed, 08 Dec 2021 19:38:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:38:54: 26000000 INFO @ Wed, 08 Dec 2021 19:39:00: 27000000 INFO @ Wed, 08 Dec 2021 19:39:05: 28000000 INFO @ Wed, 08 Dec 2021 19:39:11: 29000000 INFO @ Wed, 08 Dec 2021 19:39:15: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:39:15: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:39:15: #1 total tags in treatment: 13715814 INFO @ Wed, 08 Dec 2021 19:39:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:39:15: #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 19:39:15: #1 tags after filtering in treatment: 12701913 INFO @ Wed, 08 Dec 2021 19:39:15: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 19:39:15: #1 finished! INFO @ Wed, 08 Dec 2021 19:39:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:39:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:39:16: #2 number of paired peaks: 329 WARNING @ Wed, 08 Dec 2021 19:39:16: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Wed, 08 Dec 2021 19:39:16: start model_add_line... INFO @ Wed, 08 Dec 2021 19:39:16: start X-correlation... INFO @ Wed, 08 Dec 2021 19:39:16: end of X-cor INFO @ Wed, 08 Dec 2021 19:39:16: #2 finished! INFO @ Wed, 08 Dec 2021 19:39:16: #2 predicted fragment length is 133 bps INFO @ Wed, 08 Dec 2021 19:39:16: #2 alternative fragment length(s) may be 3,133,150,176 bps INFO @ Wed, 08 Dec 2021 19:39:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.20_model.r INFO @ Wed, 08 Dec 2021 19:39:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:39:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:39:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:39:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:39:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.10_summits.bed INFO @ Wed, 08 Dec 2021 19:39:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:39:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976739/SRX8976739.20_summits.bed INFO @ Wed, 08 Dec 2021 19:39:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling