Job ID = 6497334 SRX = SRX1353660 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:26:34 prefetch.2.10.7: 1) Downloading 'SRR2722814'... 2020-06-25T21:26:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:28:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:28:51 prefetch.2.10.7: 1) 'SRR2722814' was downloaded successfully Read 14720643 spots for SRR2722814/SRR2722814.sra Written 14720643 spots for SRR2722814/SRR2722814.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:34 14720643 reads; of these: 14720643 (100.00%) were paired; of these: 746072 (5.07%) aligned concordantly 0 times 11867477 (80.62%) aligned concordantly exactly 1 time 2107094 (14.31%) aligned concordantly >1 times ---- 746072 pairs aligned concordantly 0 times; of these: 353621 (47.40%) aligned discordantly 1 time ---- 392451 pairs aligned 0 times concordantly or discordantly; of these: 784902 mates make up the pairs; of these: 410109 (52.25%) aligned 0 times 214720 (27.36%) aligned exactly 1 time 160073 (20.39%) aligned >1 times 98.61% overall alignment rate Time searching: 00:16:35 Overall time: 00:16:35 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] 183421 / 14181333 = 0.0129 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 06:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.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 06:58:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:58:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:58:21: 1000000 INFO @ Fri, 26 Jun 2020 06:58:27: 2000000 INFO @ Fri, 26 Jun 2020 06:58:33: 3000000 INFO @ Fri, 26 Jun 2020 06:58:39: 4000000 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 06:58:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.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 06:58:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:58:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:58:46: 5000000 INFO @ Fri, 26 Jun 2020 06:58:51: 1000000 INFO @ Fri, 26 Jun 2020 06:58:53: 6000000 INFO @ Fri, 26 Jun 2020 06:58:58: 2000000 INFO @ Fri, 26 Jun 2020 06:59:00: 7000000 INFO @ Fri, 26 Jun 2020 06:59:05: 3000000 INFO @ Fri, 26 Jun 2020 06:59:07: 8000000 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 06:59:12: 4000000 INFO @ Fri, 26 Jun 2020 06:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.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 06:59:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:59:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:59:14: 9000000 INFO @ Fri, 26 Jun 2020 06:59:19: 5000000 INFO @ Fri, 26 Jun 2020 06:59:21: 10000000 INFO @ Fri, 26 Jun 2020 06:59:21: 1000000 INFO @ Fri, 26 Jun 2020 06:59:27: 6000000 INFO @ Fri, 26 Jun 2020 06:59:29: 11000000 INFO @ Fri, 26 Jun 2020 06:59:29: 2000000 INFO @ Fri, 26 Jun 2020 06:59:34: 7000000 INFO @ Fri, 26 Jun 2020 06:59:36: 12000000 INFO @ Fri, 26 Jun 2020 06:59:36: 3000000 INFO @ Fri, 26 Jun 2020 06:59:42: 8000000 INFO @ Fri, 26 Jun 2020 06:59:44: 13000000 INFO @ Fri, 26 Jun 2020 06:59:44: 4000000 INFO @ Fri, 26 Jun 2020 06:59:49: 9000000 INFO @ Fri, 26 Jun 2020 06:59:51: 14000000 INFO @ Fri, 26 Jun 2020 06:59:51: 5000000 INFO @ Fri, 26 Jun 2020 06:59:56: 10000000 INFO @ Fri, 26 Jun 2020 06:59:58: 15000000 INFO @ Fri, 26 Jun 2020 06:59:59: 6000000 INFO @ Fri, 26 Jun 2020 07:00:04: 11000000 INFO @ Fri, 26 Jun 2020 07:00:06: 16000000 INFO @ Fri, 26 Jun 2020 07:00:08: 7000000 INFO @ Fri, 26 Jun 2020 07:00:11: 12000000 INFO @ Fri, 26 Jun 2020 07:00:14: 17000000 INFO @ Fri, 26 Jun 2020 07:00:16: 8000000 INFO @ Fri, 26 Jun 2020 07:00:19: 13000000 INFO @ Fri, 26 Jun 2020 07:00:21: 18000000 INFO @ Fri, 26 Jun 2020 07:00:23: 9000000 INFO @ Fri, 26 Jun 2020 07:00:26: 14000000 INFO @ Fri, 26 Jun 2020 07:00:29: 19000000 INFO @ Fri, 26 Jun 2020 07:00:32: 10000000 INFO @ Fri, 26 Jun 2020 07:00:33: 15000000 INFO @ Fri, 26 Jun 2020 07:00:37: 20000000 INFO @ Fri, 26 Jun 2020 07:00:39: 11000000 INFO @ Fri, 26 Jun 2020 07:00:40: 16000000 INFO @ Fri, 26 Jun 2020 07:00:44: 21000000 INFO @ Fri, 26 Jun 2020 07:00:47: 12000000 INFO @ Fri, 26 Jun 2020 07:00:47: 17000000 INFO @ Fri, 26 Jun 2020 07:00:52: 22000000 INFO @ Fri, 26 Jun 2020 07:00:54: 13000000 INFO @ Fri, 26 Jun 2020 07:00:55: 18000000 INFO @ Fri, 26 Jun 2020 07:00:59: 23000000 INFO @ Fri, 26 Jun 2020 07:01:02: 14000000 INFO @ Fri, 26 Jun 2020 07:01:03: 19000000 INFO @ Fri, 26 Jun 2020 07:01:07: 24000000 INFO @ Fri, 26 Jun 2020 07:01:10: 15000000 INFO @ Fri, 26 Jun 2020 07:01:11: 20000000 INFO @ Fri, 26 Jun 2020 07:01:15: 25000000 INFO @ Fri, 26 Jun 2020 07:01:18: 16000000 INFO @ Fri, 26 Jun 2020 07:01:19: 21000000 INFO @ Fri, 26 Jun 2020 07:01:23: 26000000 INFO @ Fri, 26 Jun 2020 07:01:27: 17000000 INFO @ Fri, 26 Jun 2020 07:01:27: 22000000 INFO @ Fri, 26 Jun 2020 07:01:31: 27000000 INFO @ Fri, 26 Jun 2020 07:01:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:01:35: 23000000 INFO @ Fri, 26 Jun 2020 07:01:39: 28000000 INFO @ Fri, 26 Jun 2020 07:01:43: 19000000 INFO @ Fri, 26 Jun 2020 07:01:43: 24000000 INFO @ Fri, 26 Jun 2020 07:01:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:01:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:01:44: #1 total tags in treatment: 13792117 INFO @ Fri, 26 Jun 2020 07:01:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:01:44: #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 07:01:44: #1 tags after filtering in treatment: 12667697 INFO @ Fri, 26 Jun 2020 07:01:44: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:01:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:01:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:01:45: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 07:01:45: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 07:01:45: start model_add_line... INFO @ Fri, 26 Jun 2020 07:01:45: start X-correlation... INFO @ Fri, 26 Jun 2020 07:01:45: end of X-cor INFO @ Fri, 26 Jun 2020 07:01:45: #2 finished! INFO @ Fri, 26 Jun 2020 07:01:45: #2 predicted fragment length is 142 bps INFO @ Fri, 26 Jun 2020 07:01:45: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 26 Jun 2020 07:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.05_model.r INFO @ Fri, 26 Jun 2020 07:01:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:01:51: 25000000 INFO @ Fri, 26 Jun 2020 07:01:51: 20000000 INFO @ Fri, 26 Jun 2020 07:01:58: 26000000 INFO @ Fri, 26 Jun 2020 07:01:59: 21000000 INFO @ Fri, 26 Jun 2020 07:02:06: 27000000 INFO @ Fri, 26 Jun 2020 07:02:07: 22000000 INFO @ Fri, 26 Jun 2020 07:02:13: 28000000 INFO @ Fri, 26 Jun 2020 07:02:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:02:15: 23000000 INFO @ Fri, 26 Jun 2020 07:02:18: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:02:18: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:02:18: #1 total tags in treatment: 13792117 INFO @ Fri, 26 Jun 2020 07:02:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:18: #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 07:02:18: #1 tags after filtering in treatment: 12667697 INFO @ Fri, 26 Jun 2020 07:02:18: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:02:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:02:19: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 07:02:19: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 07:02:19: start model_add_line... INFO @ Fri, 26 Jun 2020 07:02:19: start X-correlation... INFO @ Fri, 26 Jun 2020 07:02:19: end of X-cor INFO @ Fri, 26 Jun 2020 07:02:19: #2 finished! INFO @ Fri, 26 Jun 2020 07:02:19: #2 predicted fragment length is 142 bps INFO @ Fri, 26 Jun 2020 07:02:19: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 26 Jun 2020 07:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.10_model.r INFO @ Fri, 26 Jun 2020 07:02:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:02:23: 24000000 INFO @ Fri, 26 Jun 2020 07:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.05_summits.bed INFO @ Fri, 26 Jun 2020 07:02:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (622 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:02:30: 25000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:02:37: 26000000 INFO @ Fri, 26 Jun 2020 07:02:44: 27000000 INFO @ Fri, 26 Jun 2020 07:02:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:02:51: 28000000 INFO @ Fri, 26 Jun 2020 07:02:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:02:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:02:55: #1 total tags in treatment: 13792117 INFO @ Fri, 26 Jun 2020 07:02:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:55: #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 07:02:55: #1 tags after filtering in treatment: 12667697 INFO @ Fri, 26 Jun 2020 07:02:55: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:02:55: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:02:56: #2 number of paired peaks: 331 WARNING @ Fri, 26 Jun 2020 07:02:56: Fewer paired peaks (331) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 331 pairs to build model! INFO @ Fri, 26 Jun 2020 07:02:56: start model_add_line... INFO @ Fri, 26 Jun 2020 07:02:56: start X-correlation... INFO @ Fri, 26 Jun 2020 07:02:56: end of X-cor INFO @ Fri, 26 Jun 2020 07:02:56: #2 finished! INFO @ Fri, 26 Jun 2020 07:02:56: #2 predicted fragment length is 142 bps INFO @ Fri, 26 Jun 2020 07:02:56: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 26 Jun 2020 07:02:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.20_model.r INFO @ Fri, 26 Jun 2020 07:02:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:11: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.10_summits.bed INFO @ Fri, 26 Jun 2020 07:03:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:03:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:03:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353660/SRX1353660.20_summits.bed INFO @ Fri, 26 Jun 2020 07:03:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling