Job ID = 6508011 SRX = SRX747302 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:30:48 prefetch.2.10.7: 1) Downloading 'SRR1635000'... 2020-06-26T13:30:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:31:58 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:31:59 prefetch.2.10.7: 'SRR1635000' is valid 2020-06-26T13:31:59 prefetch.2.10.7: 1) 'SRR1635000' was downloaded successfully 2020-06-26T13:32:32 prefetch.2.10.7: 'SRR1635000' has 6 unresolved dependencies 2020-06-26T13:32:32 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-26T13:32:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:32:48 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:32:48 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:32:48 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-26T13:32:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:33:05 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:33:05 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:33:05 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-26T13:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:33:21 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:33:21 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:33:21 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-26T13:33:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:33:41 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:33:41 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:33:41 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-26T13:33:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:33:58 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:33:58 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-26T13:33:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-26T13:33:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:16 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:16 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 21338534 spots for SRR1635000/SRR1635000.sra Written 21338534 spots for SRR1635000/SRR1635000.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: 00:02:45 21338534 reads; of these: 21338534 (100.00%) were unpaired; of these: 2672380 (12.52%) aligned 0 times 16314359 (76.45%) aligned exactly 1 time 2351795 (11.02%) aligned >1 times 87.48% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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 8 files... [bam_rmdupse_core] 3989764 / 18666154 = 0.2137 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 22:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.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 22:41:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:41:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:42:01: 1000000 INFO @ Fri, 26 Jun 2020 22:42:06: 2000000 INFO @ Fri, 26 Jun 2020 22:42:11: 3000000 INFO @ Fri, 26 Jun 2020 22:42:16: 4000000 INFO @ Fri, 26 Jun 2020 22:42:21: 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 22:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.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 22:42:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:42:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:42:26: 6000000 INFO @ Fri, 26 Jun 2020 22:42:32: 1000000 INFO @ Fri, 26 Jun 2020 22:42:32: 7000000 INFO @ Fri, 26 Jun 2020 22:42:38: 8000000 INFO @ Fri, 26 Jun 2020 22:42:38: 2000000 INFO @ Fri, 26 Jun 2020 22:42:43: 9000000 INFO @ Fri, 26 Jun 2020 22:42:45: 3000000 INFO @ Fri, 26 Jun 2020 22:42:49: 10000000 INFO @ Fri, 26 Jun 2020 22:42:51: 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 22:42:54: 11000000 INFO @ Fri, 26 Jun 2020 22:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.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 22:42:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:42:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:42:58: 5000000 INFO @ Fri, 26 Jun 2020 22:43:00: 12000000 INFO @ Fri, 26 Jun 2020 22:43:02: 1000000 INFO @ Fri, 26 Jun 2020 22:43:04: 6000000 INFO @ Fri, 26 Jun 2020 22:43:05: 13000000 INFO @ Fri, 26 Jun 2020 22:43:08: 2000000 INFO @ Fri, 26 Jun 2020 22:43:11: 7000000 INFO @ Fri, 26 Jun 2020 22:43:11: 14000000 INFO @ Fri, 26 Jun 2020 22:43:14: 3000000 INFO @ Fri, 26 Jun 2020 22:43:15: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:43:15: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:43:15: #1 total tags in treatment: 14676390 INFO @ Fri, 26 Jun 2020 22:43:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:43:15: #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 22:43:15: #1 tags after filtering in treatment: 14676390 INFO @ Fri, 26 Jun 2020 22:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:43:15: #1 finished! INFO @ Fri, 26 Jun 2020 22:43:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:43:16: #2 number of paired peaks: 153 WARNING @ Fri, 26 Jun 2020 22:43:16: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 26 Jun 2020 22:43:16: start model_add_line... INFO @ Fri, 26 Jun 2020 22:43:16: start X-correlation... INFO @ Fri, 26 Jun 2020 22:43:16: end of X-cor INFO @ Fri, 26 Jun 2020 22:43:16: #2 finished! INFO @ Fri, 26 Jun 2020 22:43:16: #2 predicted fragment length is 83 bps INFO @ Fri, 26 Jun 2020 22:43:16: #2 alternative fragment length(s) may be 2,33,83,130,154,496,564 bps INFO @ Fri, 26 Jun 2020 22:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.05_model.r INFO @ Fri, 26 Jun 2020 22:43:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:43:17: 8000000 INFO @ Fri, 26 Jun 2020 22:43:21: 4000000 INFO @ Fri, 26 Jun 2020 22:43:24: 9000000 INFO @ Fri, 26 Jun 2020 22:43:27: 5000000 INFO @ Fri, 26 Jun 2020 22:43:30: 10000000 INFO @ Fri, 26 Jun 2020 22:43:34: 6000000 INFO @ Fri, 26 Jun 2020 22:43:37: 11000000 INFO @ Fri, 26 Jun 2020 22:43:40: 7000000 INFO @ Fri, 26 Jun 2020 22:43:43: 12000000 INFO @ Fri, 26 Jun 2020 22:43:47: 8000000 INFO @ Fri, 26 Jun 2020 22:43:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:43:49: 13000000 INFO @ Fri, 26 Jun 2020 22:43:54: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:43:56: 14000000 INFO @ Fri, 26 Jun 2020 22:44:00: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:44:00: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:44:00: #1 total tags in treatment: 14676390 INFO @ Fri, 26 Jun 2020 22:44:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:44:00: #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 22:44:00: 10000000 INFO @ Fri, 26 Jun 2020 22:44:00: #1 tags after filtering in treatment: 14676390 INFO @ Fri, 26 Jun 2020 22:44:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:44:00: #1 finished! INFO @ Fri, 26 Jun 2020 22:44:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:44:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:44:01: #2 number of paired peaks: 153 WARNING @ Fri, 26 Jun 2020 22:44:01: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 26 Jun 2020 22:44:01: start model_add_line... INFO @ Fri, 26 Jun 2020 22:44:01: start X-correlation... INFO @ Fri, 26 Jun 2020 22:44:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:44:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:44:02: #2 predicted fragment length is 83 bps INFO @ Fri, 26 Jun 2020 22:44:02: #2 alternative fragment length(s) may be 2,33,83,130,154,496,564 bps INFO @ Fri, 26 Jun 2020 22:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.10_model.r INFO @ Fri, 26 Jun 2020 22:44:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:44:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:44:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:44:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.05_summits.bed INFO @ Fri, 26 Jun 2020 22:44:03: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (11046 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:44:06: 11000000 INFO @ Fri, 26 Jun 2020 22:44:12: 12000000 INFO @ Fri, 26 Jun 2020 22:44:18: 13000000 INFO @ Fri, 26 Jun 2020 22:44:24: 14000000 INFO @ Fri, 26 Jun 2020 22:44:28: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:44:28: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:44:28: #1 total tags in treatment: 14676390 INFO @ Fri, 26 Jun 2020 22:44:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:44:28: #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 22:44:28: #1 tags after filtering in treatment: 14676390 INFO @ Fri, 26 Jun 2020 22:44:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:44:28: #1 finished! INFO @ Fri, 26 Jun 2020 22:44:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:44:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:44:29: #2 number of paired peaks: 153 WARNING @ Fri, 26 Jun 2020 22:44:29: Fewer paired peaks (153) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 153 pairs to build model! INFO @ Fri, 26 Jun 2020 22:44:29: start model_add_line... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:44:29: start X-correlation... INFO @ Fri, 26 Jun 2020 22:44:29: end of X-cor INFO @ Fri, 26 Jun 2020 22:44:29: #2 finished! INFO @ Fri, 26 Jun 2020 22:44:29: #2 predicted fragment length is 83 bps INFO @ Fri, 26 Jun 2020 22:44:29: #2 alternative fragment length(s) may be 2,33,83,130,154,496,564 bps INFO @ Fri, 26 Jun 2020 22:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.20_model.r INFO @ Fri, 26 Jun 2020 22:44:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:44:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:44:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:44:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:44:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.10_summits.bed INFO @ Fri, 26 Jun 2020 22:44:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4030 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:45:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:45:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:45:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:45:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX747302/SRX747302.20_summits.bed INFO @ Fri, 26 Jun 2020 22:45:17: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (684 records, 4 fields): 2 millis CompletedMACS2peakCalling