Job ID = 6507768 SRX = SRX4085355 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:38:41 prefetch.2.10.7: 1) Downloading 'SRR7167384'... 2020-06-26T13:38:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:47:20 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:47:20 prefetch.2.10.7: 1) 'SRR7167384' was downloaded successfully Read 33188741 spots for SRR7167384/SRR7167384.sra Written 33188741 spots for SRR7167384/SRR7167384.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: 00:28:48 33188741 reads; of these: 33188741 (100.00%) were paired; of these: 3587101 (10.81%) aligned concordantly 0 times 25813942 (77.78%) aligned concordantly exactly 1 time 3787698 (11.41%) aligned concordantly >1 times ---- 3587101 pairs aligned concordantly 0 times; of these: 820601 (22.88%) aligned discordantly 1 time ---- 2766500 pairs aligned 0 times concordantly or discordantly; of these: 5533000 mates make up the pairs; of these: 3187949 (57.62%) aligned 0 times 1731522 (31.29%) aligned exactly 1 time 613529 (11.09%) aligned >1 times 95.20% overall alignment rate Time searching: 00:28:48 Overall time: 00:28:48 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 28 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] 19013175 / 29900422 = 0.6359 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 23:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.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 23:34:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:34:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:34:22: 1000000 INFO @ Fri, 26 Jun 2020 23:34:29: 2000000 INFO @ Fri, 26 Jun 2020 23:34:36: 3000000 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 23:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.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 23:34:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:34:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:34:43: 4000000 INFO @ Fri, 26 Jun 2020 23:34:49: 1000000 INFO @ Fri, 26 Jun 2020 23:34:51: 5000000 INFO @ Fri, 26 Jun 2020 23:34:56: 2000000 INFO @ Fri, 26 Jun 2020 23:34:58: 6000000 INFO @ Fri, 26 Jun 2020 23:35:02: 3000000 INFO @ Fri, 26 Jun 2020 23:35:06: 7000000 INFO @ Fri, 26 Jun 2020 23:35:09: 4000000 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 23:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.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 23:35:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:35:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:35:13: 8000000 INFO @ Fri, 26 Jun 2020 23:35:16: 5000000 INFO @ Fri, 26 Jun 2020 23:35:19: 1000000 INFO @ Fri, 26 Jun 2020 23:35:20: 9000000 INFO @ Fri, 26 Jun 2020 23:35:23: 6000000 INFO @ Fri, 26 Jun 2020 23:35:26: 2000000 INFO @ Fri, 26 Jun 2020 23:35:28: 10000000 INFO @ Fri, 26 Jun 2020 23:35:30: 7000000 INFO @ Fri, 26 Jun 2020 23:35:33: 3000000 INFO @ Fri, 26 Jun 2020 23:35:35: 11000000 INFO @ Fri, 26 Jun 2020 23:35:37: 8000000 INFO @ Fri, 26 Jun 2020 23:35:40: 4000000 INFO @ Fri, 26 Jun 2020 23:35:43: 12000000 INFO @ Fri, 26 Jun 2020 23:35:44: 9000000 INFO @ Fri, 26 Jun 2020 23:35:47: 5000000 INFO @ Fri, 26 Jun 2020 23:35:50: 13000000 INFO @ Fri, 26 Jun 2020 23:35:52: 10000000 INFO @ Fri, 26 Jun 2020 23:35:55: 6000000 INFO @ Fri, 26 Jun 2020 23:35:57: 14000000 INFO @ Fri, 26 Jun 2020 23:35:59: 11000000 INFO @ Fri, 26 Jun 2020 23:36:02: 7000000 INFO @ Fri, 26 Jun 2020 23:36:05: 15000000 INFO @ Fri, 26 Jun 2020 23:36:06: 12000000 INFO @ Fri, 26 Jun 2020 23:36:09: 8000000 INFO @ Fri, 26 Jun 2020 23:36:12: 16000000 INFO @ Fri, 26 Jun 2020 23:36:13: 13000000 INFO @ Fri, 26 Jun 2020 23:36:16: 9000000 INFO @ Fri, 26 Jun 2020 23:36:20: 14000000 INFO @ Fri, 26 Jun 2020 23:36:20: 17000000 INFO @ Fri, 26 Jun 2020 23:36:23: 10000000 INFO @ Fri, 26 Jun 2020 23:36:27: 15000000 INFO @ Fri, 26 Jun 2020 23:36:27: 18000000 INFO @ Fri, 26 Jun 2020 23:36:30: 11000000 INFO @ Fri, 26 Jun 2020 23:36:34: 16000000 INFO @ Fri, 26 Jun 2020 23:36:34: 19000000 INFO @ Fri, 26 Jun 2020 23:36:36: 12000000 INFO @ Fri, 26 Jun 2020 23:36:40: 17000000 INFO @ Fri, 26 Jun 2020 23:36:42: 20000000 INFO @ Fri, 26 Jun 2020 23:36:43: 13000000 INFO @ Fri, 26 Jun 2020 23:36:47: 18000000 INFO @ Fri, 26 Jun 2020 23:36:49: 21000000 INFO @ Fri, 26 Jun 2020 23:36:50: 14000000 INFO @ Fri, 26 Jun 2020 23:36:54: 19000000 INFO @ Fri, 26 Jun 2020 23:36:56: 22000000 INFO @ Fri, 26 Jun 2020 23:36:57: 15000000 INFO @ Fri, 26 Jun 2020 23:37:01: 20000000 INFO @ Fri, 26 Jun 2020 23:37:04: 23000000 INFO @ Fri, 26 Jun 2020 23:37:04: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:37:08: 21000000 INFO @ Fri, 26 Jun 2020 23:37:11: 24000000 INFO @ Fri, 26 Jun 2020 23:37:11: 17000000 INFO @ Fri, 26 Jun 2020 23:37:15: 22000000 INFO @ Fri, 26 Jun 2020 23:37:18: 18000000 INFO @ Fri, 26 Jun 2020 23:37:18: 25000000 INFO @ Fri, 26 Jun 2020 23:37:19: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:37:19: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:37:19: #1 total tags in treatment: 10776633 INFO @ Fri, 26 Jun 2020 23:37:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:19: #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 23:37:20: #1 tags after filtering in treatment: 9638073 INFO @ Fri, 26 Jun 2020 23:37:20: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:37:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:20: #2 number of paired peaks: 351 WARNING @ Fri, 26 Jun 2020 23:37:20: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Fri, 26 Jun 2020 23:37:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:20: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:20: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:20: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:20: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 23:37:20: #2 alternative fragment length(s) may be 4,111,118 bps INFO @ Fri, 26 Jun 2020 23:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.05_model.r INFO @ Fri, 26 Jun 2020 23:37:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:37:22: 23000000 INFO @ Fri, 26 Jun 2020 23:37:25: 19000000 INFO @ Fri, 26 Jun 2020 23:37:29: 24000000 INFO @ Fri, 26 Jun 2020 23:37:31: 20000000 INFO @ Fri, 26 Jun 2020 23:37:35: 25000000 INFO @ Fri, 26 Jun 2020 23:37:36: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:37:36: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:37:36: #1 total tags in treatment: 10776633 INFO @ Fri, 26 Jun 2020 23:37:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:36: #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 23:37:37: #1 tags after filtering in treatment: 9638073 INFO @ Fri, 26 Jun 2020 23:37:37: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:37:37: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:37: #2 number of paired peaks: 351 WARNING @ Fri, 26 Jun 2020 23:37:37: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Fri, 26 Jun 2020 23:37:37: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:37: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:37: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:37: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:37: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 23:37:37: #2 alternative fragment length(s) may be 4,111,118 bps INFO @ Fri, 26 Jun 2020 23:37:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.10_model.r INFO @ Fri, 26 Jun 2020 23:37:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:37:38: 21000000 INFO @ Fri, 26 Jun 2020 23:37:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:37:44: 22000000 INFO @ Fri, 26 Jun 2020 23:37:50: 23000000 INFO @ Fri, 26 Jun 2020 23:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:37:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:37:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.05_summits.bed INFO @ Fri, 26 Jun 2020 23:37:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:37:56: 24000000 INFO @ Fri, 26 Jun 2020 23:37:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:38:02: 25000000 INFO @ Fri, 26 Jun 2020 23:38:03: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:38:03: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:38:03: #1 total tags in treatment: 10776633 INFO @ Fri, 26 Jun 2020 23:38:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:38:03: #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 23:38:03: #1 tags after filtering in treatment: 9638073 INFO @ Fri, 26 Jun 2020 23:38:03: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:38:03: #1 finished! INFO @ Fri, 26 Jun 2020 23:38:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:38:03: #2 number of paired peaks: 351 WARNING @ Fri, 26 Jun 2020 23:38:03: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Fri, 26 Jun 2020 23:38:03: start model_add_line... INFO @ Fri, 26 Jun 2020 23:38:03: start X-correlation... INFO @ Fri, 26 Jun 2020 23:38:03: end of X-cor INFO @ Fri, 26 Jun 2020 23:38:03: #2 finished! INFO @ Fri, 26 Jun 2020 23:38:03: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 23:38:03: #2 alternative fragment length(s) may be 4,111,118 bps INFO @ Fri, 26 Jun 2020 23:38:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.20_model.r INFO @ Fri, 26 Jun 2020 23:38:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:38:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.10_summits.bed INFO @ Fri, 26 Jun 2020 23:38:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:38:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085355/SRX4085355.20_summits.bed INFO @ Fri, 26 Jun 2020 23:38:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling