Job ID = 6367830 SRX = SRX4085398 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:20 prefetch.2.10.7: 1) Downloading 'SRR7167427'... 2020-06-15T23:35:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:11 prefetch.2.10.7: 1) 'SRR7167427' was downloaded successfully Read 38357635 spots for SRR7167427/SRR7167427.sra Written 38357635 spots for SRR7167427/SRR7167427.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: 00:31:03 38357635 reads; of these: 38357635 (100.00%) were paired; of these: 3589044 (9.36%) aligned concordantly 0 times 30832379 (80.38%) aligned concordantly exactly 1 time 3936212 (10.26%) aligned concordantly >1 times ---- 3589044 pairs aligned concordantly 0 times; of these: 1399458 (38.99%) aligned discordantly 1 time ---- 2189586 pairs aligned 0 times concordantly or discordantly; of these: 4379172 mates make up the pairs; of these: 2667306 (60.91%) aligned 0 times 1098540 (25.09%) aligned exactly 1 time 613326 (14.01%) aligned >1 times 96.52% overall alignment rate Time searching: 00:31:03 Overall time: 00:31:03 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 32 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] 21618444 / 35055148 = 0.6167 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 @ Tue, 16 Jun 2020 09:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.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 @ Tue, 16 Jun 2020 09:40:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:37: 1000000 INFO @ Tue, 16 Jun 2020 09:40:43: 2000000 INFO @ Tue, 16 Jun 2020 09:40:49: 3000000 INFO @ Tue, 16 Jun 2020 09:40:55: 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 @ Tue, 16 Jun 2020 09:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.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 @ Tue, 16 Jun 2020 09:41:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:01: 5000000 INFO @ Tue, 16 Jun 2020 09:41:09: 6000000 INFO @ Tue, 16 Jun 2020 09:41:09: 1000000 INFO @ Tue, 16 Jun 2020 09:41:16: 7000000 INFO @ Tue, 16 Jun 2020 09:41:18: 2000000 INFO @ Tue, 16 Jun 2020 09:41:23: 8000000 INFO @ Tue, 16 Jun 2020 09:41:26: 3000000 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 @ Tue, 16 Jun 2020 09:41:31: 9000000 INFO @ Tue, 16 Jun 2020 09:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.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 @ Tue, 16 Jun 2020 09:41:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:34: 4000000 INFO @ Tue, 16 Jun 2020 09:41:38: 10000000 INFO @ Tue, 16 Jun 2020 09:41:39: 1000000 INFO @ Tue, 16 Jun 2020 09:41:41: 5000000 INFO @ Tue, 16 Jun 2020 09:41:46: 11000000 INFO @ Tue, 16 Jun 2020 09:41:47: 2000000 INFO @ Tue, 16 Jun 2020 09:41:49: 6000000 INFO @ Tue, 16 Jun 2020 09:41:53: 12000000 INFO @ Tue, 16 Jun 2020 09:41:55: 3000000 INFO @ Tue, 16 Jun 2020 09:41:57: 7000000 INFO @ Tue, 16 Jun 2020 09:42:01: 13000000 INFO @ Tue, 16 Jun 2020 09:42:03: 4000000 INFO @ Tue, 16 Jun 2020 09:42:05: 8000000 INFO @ Tue, 16 Jun 2020 09:42:08: 14000000 INFO @ Tue, 16 Jun 2020 09:42:10: 5000000 INFO @ Tue, 16 Jun 2020 09:42:13: 9000000 INFO @ Tue, 16 Jun 2020 09:42:16: 15000000 INFO @ Tue, 16 Jun 2020 09:42:18: 6000000 INFO @ Tue, 16 Jun 2020 09:42:21: 10000000 INFO @ Tue, 16 Jun 2020 09:42:23: 16000000 INFO @ Tue, 16 Jun 2020 09:42:25: 7000000 INFO @ Tue, 16 Jun 2020 09:42:29: 11000000 INFO @ Tue, 16 Jun 2020 09:42:31: 17000000 INFO @ Tue, 16 Jun 2020 09:42:33: 8000000 INFO @ Tue, 16 Jun 2020 09:42:37: 12000000 INFO @ Tue, 16 Jun 2020 09:42:38: 18000000 INFO @ Tue, 16 Jun 2020 09:42:41: 9000000 INFO @ Tue, 16 Jun 2020 09:42:44: 13000000 INFO @ Tue, 16 Jun 2020 09:42:46: 19000000 INFO @ Tue, 16 Jun 2020 09:42:49: 10000000 INFO @ Tue, 16 Jun 2020 09:42:52: 14000000 INFO @ Tue, 16 Jun 2020 09:42:53: 20000000 INFO @ Tue, 16 Jun 2020 09:42:56: 11000000 INFO @ Tue, 16 Jun 2020 09:43:00: 15000000 INFO @ Tue, 16 Jun 2020 09:43:01: 21000000 INFO @ Tue, 16 Jun 2020 09:43:04: 12000000 INFO @ Tue, 16 Jun 2020 09:43:08: 16000000 INFO @ Tue, 16 Jun 2020 09:43:08: 22000000 INFO @ Tue, 16 Jun 2020 09:43:12: 13000000 INFO @ Tue, 16 Jun 2020 09:43:16: 23000000 INFO @ Tue, 16 Jun 2020 09:43:16: 17000000 INFO @ Tue, 16 Jun 2020 09:43:20: 14000000 INFO @ Tue, 16 Jun 2020 09:43:23: 24000000 INFO @ Tue, 16 Jun 2020 09:43:24: 18000000 INFO @ Tue, 16 Jun 2020 09:43:28: 15000000 INFO @ Tue, 16 Jun 2020 09:43:31: 25000000 INFO @ Tue, 16 Jun 2020 09:43:32: 19000000 INFO @ Tue, 16 Jun 2020 09:43:35: 16000000 INFO @ Tue, 16 Jun 2020 09:43:39: 26000000 INFO @ Tue, 16 Jun 2020 09:43:40: 20000000 INFO @ Tue, 16 Jun 2020 09:43:43: 17000000 INFO @ Tue, 16 Jun 2020 09:43:46: 27000000 INFO @ Tue, 16 Jun 2020 09:43:48: 21000000 INFO @ Tue, 16 Jun 2020 09:43:51: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:43:54: 28000000 INFO @ Tue, 16 Jun 2020 09:43:56: 22000000 INFO @ Tue, 16 Jun 2020 09:43:58: 19000000 INFO @ Tue, 16 Jun 2020 09:44:01: 29000000 INFO @ Tue, 16 Jun 2020 09:44:03: 23000000 INFO @ Tue, 16 Jun 2020 09:44:06: 20000000 INFO @ Tue, 16 Jun 2020 09:44:08: 30000000 INFO @ Tue, 16 Jun 2020 09:44:11: 24000000 INFO @ Tue, 16 Jun 2020 09:44:14: 21000000 INFO @ Tue, 16 Jun 2020 09:44:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:44:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:44:14: #1 total tags in treatment: 13325562 INFO @ Tue, 16 Jun 2020 09:44:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:44:14: #1 tags after filtering in treatment: 11187502 INFO @ Tue, 16 Jun 2020 09:44:14: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 16 Jun 2020 09:44:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:15: #2 number of paired peaks: 410 WARNING @ Tue, 16 Jun 2020 09:44:15: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:15: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 09:44:15: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 09:44:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.05_model.r INFO @ Tue, 16 Jun 2020 09:44:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:19: 25000000 INFO @ Tue, 16 Jun 2020 09:44:21: 22000000 INFO @ Tue, 16 Jun 2020 09:44:27: 26000000 INFO @ Tue, 16 Jun 2020 09:44:29: 23000000 INFO @ Tue, 16 Jun 2020 09:44:35: 27000000 INFO @ Tue, 16 Jun 2020 09:44:36: 24000000 INFO @ Tue, 16 Jun 2020 09:44:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:43: 28000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:44:44: 25000000 INFO @ Tue, 16 Jun 2020 09:44:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3923 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:50: 29000000 INFO @ Tue, 16 Jun 2020 09:44:51: 26000000 INFO @ Tue, 16 Jun 2020 09:44:58: 30000000 INFO @ Tue, 16 Jun 2020 09:44:59: 27000000 INFO @ Tue, 16 Jun 2020 09:45:04: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:45:04: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:45:04: #1 total tags in treatment: 13325562 INFO @ Tue, 16 Jun 2020 09:45:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:45:05: #1 tags after filtering in treatment: 11187502 INFO @ Tue, 16 Jun 2020 09:45:05: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 16 Jun 2020 09:45:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:05: #2 number of paired peaks: 410 WARNING @ Tue, 16 Jun 2020 09:45:05: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:05: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 09:45:05: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 09:45:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.10_model.r INFO @ Tue, 16 Jun 2020 09:45:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:06: 28000000 INFO @ Tue, 16 Jun 2020 09:45:12: 29000000 INFO @ Tue, 16 Jun 2020 09:45:18: 30000000 INFO @ Tue, 16 Jun 2020 09:45:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:45:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:45:23: #1 total tags in treatment: 13325562 INFO @ Tue, 16 Jun 2020 09:45:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:45:23: #1 tags after filtering in treatment: 11187502 INFO @ Tue, 16 Jun 2020 09:45:23: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 16 Jun 2020 09:45:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:24: #2 number of paired peaks: 410 WARNING @ Tue, 16 Jun 2020 09:45:24: Fewer paired peaks (410) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 410 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:24: #2 predicted fragment length is 110 bps INFO @ Tue, 16 Jun 2020 09:45:24: #2 alternative fragment length(s) may be 4,110 bps INFO @ Tue, 16 Jun 2020 09:45:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.20_model.r INFO @ Tue, 16 Jun 2020 09:45:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.10_summits.bed INFO @ Tue, 16 Jun 2020 09:45:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2054 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085398/SRX4085398.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (772 records, 4 fields): 2 millis CompletedMACS2peakCalling