Job ID = 6497380 SRX = SRX4085357 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:15:44 prefetch.2.10.7: 1) Downloading 'SRR7167386'... 2020-06-25T22:15:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:21:21 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:21:21 prefetch.2.10.7: 1) 'SRR7167386' was downloaded successfully Read 19379584 spots for SRR7167386/SRR7167386.sra Written 19379584 spots for SRR7167386/SRR7167386.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:03 19379584 reads; of these: 19379584 (100.00%) were paired; of these: 591747 (3.05%) aligned concordantly 0 times 16382606 (84.54%) aligned concordantly exactly 1 time 2405231 (12.41%) aligned concordantly >1 times ---- 591747 pairs aligned concordantly 0 times; of these: 73964 (12.50%) aligned discordantly 1 time ---- 517783 pairs aligned 0 times concordantly or discordantly; of these: 1035566 mates make up the pairs; of these: 628131 (60.66%) aligned 0 times 314042 (30.33%) aligned exactly 1 time 93393 (9.02%) aligned >1 times 98.38% overall alignment rate Time searching: 00:19:03 Overall time: 00:19:03 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 16 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] 4252975 / 18827094 = 0.2259 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.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 @ Fri, 26 Jun 2020 07:54:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:54:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:54:33: 1000000 INFO @ Fri, 26 Jun 2020 07:54:37: 2000000 INFO @ Fri, 26 Jun 2020 07:54:42: 3000000 INFO @ Fri, 26 Jun 2020 07:54:47: 4000000 INFO @ Fri, 26 Jun 2020 07:54:51: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:54:56: 6000000 INFO @ Fri, 26 Jun 2020 07:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.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 @ Fri, 26 Jun 2020 07:54:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:54:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:55:01: 7000000 INFO @ Fri, 26 Jun 2020 07:55:03: 1000000 INFO @ Fri, 26 Jun 2020 07:55:06: 8000000 INFO @ Fri, 26 Jun 2020 07:55:08: 2000000 INFO @ Fri, 26 Jun 2020 07:55:11: 9000000 INFO @ Fri, 26 Jun 2020 07:55:13: 3000000 INFO @ Fri, 26 Jun 2020 07:55:16: 10000000 INFO @ Fri, 26 Jun 2020 07:55:19: 4000000 INFO @ Fri, 26 Jun 2020 07:55:21: 11000000 INFO @ Fri, 26 Jun 2020 07:55:24: 5000000 INFO @ Fri, 26 Jun 2020 07:55:26: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:55:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.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 @ Fri, 26 Jun 2020 07:55:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:55:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:55:29: 6000000 INFO @ Fri, 26 Jun 2020 07:55:31: 13000000 INFO @ Fri, 26 Jun 2020 07:55:33: 1000000 INFO @ Fri, 26 Jun 2020 07:55:34: 7000000 INFO @ Fri, 26 Jun 2020 07:55:36: 14000000 INFO @ Fri, 26 Jun 2020 07:55:38: 2000000 INFO @ Fri, 26 Jun 2020 07:55:39: 8000000 INFO @ Fri, 26 Jun 2020 07:55:41: 15000000 INFO @ Fri, 26 Jun 2020 07:55:43: 3000000 INFO @ Fri, 26 Jun 2020 07:55:44: 9000000 INFO @ Fri, 26 Jun 2020 07:55:46: 16000000 INFO @ Fri, 26 Jun 2020 07:55:48: 4000000 INFO @ Fri, 26 Jun 2020 07:55:49: 10000000 INFO @ Fri, 26 Jun 2020 07:55:51: 17000000 INFO @ Fri, 26 Jun 2020 07:55:53: 5000000 INFO @ Fri, 26 Jun 2020 07:55:54: 11000000 INFO @ Fri, 26 Jun 2020 07:55:56: 18000000 INFO @ Fri, 26 Jun 2020 07:55:59: 6000000 INFO @ Fri, 26 Jun 2020 07:56:00: 12000000 INFO @ Fri, 26 Jun 2020 07:56:01: 19000000 INFO @ Fri, 26 Jun 2020 07:56:05: 7000000 INFO @ Fri, 26 Jun 2020 07:56:05: 13000000 INFO @ Fri, 26 Jun 2020 07:56:06: 20000000 INFO @ Fri, 26 Jun 2020 07:56:10: 14000000 INFO @ Fri, 26 Jun 2020 07:56:10: 8000000 INFO @ Fri, 26 Jun 2020 07:56:11: 21000000 INFO @ Fri, 26 Jun 2020 07:56:15: 15000000 INFO @ Fri, 26 Jun 2020 07:56:16: 9000000 INFO @ Fri, 26 Jun 2020 07:56:16: 22000000 INFO @ Fri, 26 Jun 2020 07:56:21: 16000000 INFO @ Fri, 26 Jun 2020 07:56:21: 23000000 INFO @ Fri, 26 Jun 2020 07:56:22: 10000000 INFO @ Fri, 26 Jun 2020 07:56:26: 17000000 INFO @ Fri, 26 Jun 2020 07:56:26: 24000000 INFO @ Fri, 26 Jun 2020 07:56:27: 11000000 INFO @ Fri, 26 Jun 2020 07:56:31: 18000000 INFO @ Fri, 26 Jun 2020 07:56:31: 25000000 INFO @ Fri, 26 Jun 2020 07:56:32: 12000000 INFO @ Fri, 26 Jun 2020 07:56:36: 19000000 INFO @ Fri, 26 Jun 2020 07:56:37: 26000000 INFO @ Fri, 26 Jun 2020 07:56:37: 13000000 INFO @ Fri, 26 Jun 2020 07:56:42: 20000000 INFO @ Fri, 26 Jun 2020 07:56:42: 27000000 INFO @ Fri, 26 Jun 2020 07:56:43: 14000000 INFO @ Fri, 26 Jun 2020 07:56:47: 21000000 INFO @ Fri, 26 Jun 2020 07:56:47: 28000000 INFO @ Fri, 26 Jun 2020 07:56:48: 15000000 INFO @ Fri, 26 Jun 2020 07:56:52: 22000000 INFO @ Fri, 26 Jun 2020 07:56:52: 29000000 INFO @ Fri, 26 Jun 2020 07:56:53: 16000000 INFO @ Fri, 26 Jun 2020 07:56:55: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:56:55: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:56:55: #1 total tags in treatment: 14543772 INFO @ Fri, 26 Jun 2020 07:56:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:56: #1 tags after filtering in treatment: 12556219 INFO @ Fri, 26 Jun 2020 07:56:56: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:56:56: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:57: #2 number of paired peaks: 298 WARNING @ Fri, 26 Jun 2020 07:56:57: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:57: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:57: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:57: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:57: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:57: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 07:56:57: #2 alternative fragment length(s) may be 4,113,127 bps INFO @ Fri, 26 Jun 2020 07:56:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.05_model.r INFO @ Fri, 26 Jun 2020 07:56:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:57: 23000000 INFO @ Fri, 26 Jun 2020 07:56:58: 17000000 INFO @ Fri, 26 Jun 2020 07:57:02: 24000000 INFO @ Fri, 26 Jun 2020 07:57:03: 18000000 INFO @ Fri, 26 Jun 2020 07:57:07: 25000000 INFO @ Fri, 26 Jun 2020 07:57:09: 19000000 INFO @ Fri, 26 Jun 2020 07:57:12: 26000000 INFO @ Fri, 26 Jun 2020 07:57:14: 20000000 INFO @ Fri, 26 Jun 2020 07:57:17: 27000000 INFO @ Fri, 26 Jun 2020 07:57:19: 21000000 INFO @ Fri, 26 Jun 2020 07:57:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:22: 28000000 INFO @ Fri, 26 Jun 2020 07:57:24: 22000000 INFO @ Fri, 26 Jun 2020 07:57:26: 29000000 INFO @ Fri, 26 Jun 2020 07:57:29: 23000000 INFO @ Fri, 26 Jun 2020 07:57:29: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:57:29: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:57:29: #1 total tags in treatment: 14543772 INFO @ Fri, 26 Jun 2020 07:57:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:57:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:57:29: #1 tags after filtering in treatment: 12556219 INFO @ Fri, 26 Jun 2020 07:57:29: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:57:29: #1 finished! INFO @ Fri, 26 Jun 2020 07:57:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:57:30: #2 number of paired peaks: 298 WARNING @ Fri, 26 Jun 2020 07:57:30: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Fri, 26 Jun 2020 07:57:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:57:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.05_summits.bed INFO @ Fri, 26 Jun 2020 07:57:30: Done! INFO @ Fri, 26 Jun 2020 07:57:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:57:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:57:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:57:30: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 07:57:30: #2 alternative fragment length(s) may be 4,113,127 bps INFO @ Fri, 26 Jun 2020 07:57:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.10_model.r INFO @ Fri, 26 Jun 2020 07:57:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:57:30: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1596 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:57:34: 24000000 INFO @ Fri, 26 Jun 2020 07:57:39: 25000000 INFO @ Fri, 26 Jun 2020 07:57:44: 26000000 INFO @ Fri, 26 Jun 2020 07:57:48: 27000000 INFO @ Fri, 26 Jun 2020 07:57:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:53: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:57:58: 29000000 INFO @ Fri, 26 Jun 2020 07:58:01: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:58:01: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:58:01: #1 total tags in treatment: 14543772 INFO @ Fri, 26 Jun 2020 07:58:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:58:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:58:02: #1 tags after filtering in treatment: 12556219 INFO @ Fri, 26 Jun 2020 07:58:02: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:58:02: #1 finished! INFO @ Fri, 26 Jun 2020 07:58:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:58:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:58:03: #2 number of paired peaks: 298 WARNING @ Fri, 26 Jun 2020 07:58:03: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Fri, 26 Jun 2020 07:58:03: start model_add_line... INFO @ Fri, 26 Jun 2020 07:58:03: start X-correlation... INFO @ Fri, 26 Jun 2020 07:58:03: end of X-cor INFO @ Fri, 26 Jun 2020 07:58:03: #2 finished! INFO @ Fri, 26 Jun 2020 07:58:03: #2 predicted fragment length is 113 bps INFO @ Fri, 26 Jun 2020 07:58:03: #2 alternative fragment length(s) may be 4,113,127 bps INFO @ Fri, 26 Jun 2020 07:58:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.20_model.r INFO @ Fri, 26 Jun 2020 07:58:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:58:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:58:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:58:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:58:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.10_summits.bed INFO @ Fri, 26 Jun 2020 07:58:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (894 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:58:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085357/SRX4085357.20_summits.bed INFO @ Fri, 26 Jun 2020 07:58:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (420 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。