Job ID = 6366668 SRX = SRX2202781 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:00:08 prefetch.2.10.7: 1) Downloading 'SRR4319287'... 2020-06-15T23:00:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:00:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:00:48 prefetch.2.10.7: 'SRR4319287' is valid 2020-06-15T23:00:48 prefetch.2.10.7: 1) 'SRR4319287' was downloaded successfully 2020-06-15T23:01:21 prefetch.2.10.7: 'SRR4319287' has 6 unresolved dependencies 2020-06-15T23:01:21 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T23:01:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:37 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:01:37 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T23:01:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:53 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:01:53 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T23:01:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:08 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:02:08 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T23:02:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:24 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:02:24 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T23:02:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:40 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:02:40 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:02:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:55 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 22115537 spots for SRR4319287/SRR4319287.sra Written 22115537 spots for SRR4319287/SRR4319287.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: 00:04:06 22115537 reads; of these: 22115537 (100.00%) were unpaired; of these: 1315527 (5.95%) aligned 0 times 16389777 (74.11%) aligned exactly 1 time 4410233 (19.94%) aligned >1 times 94.05% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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_rmdupse_core] 4273643 / 20800010 = 0.2055 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 08:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.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 08:13:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:10: 1000000 INFO @ Tue, 16 Jun 2020 08:13:16: 2000000 INFO @ Tue, 16 Jun 2020 08:13:21: 3000000 INFO @ Tue, 16 Jun 2020 08:13:27: 4000000 INFO @ Tue, 16 Jun 2020 08:13:32: 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 @ Tue, 16 Jun 2020 08:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.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 08:13:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:38: 6000000 INFO @ Tue, 16 Jun 2020 08:13:41: 1000000 INFO @ Tue, 16 Jun 2020 08:13:43: 7000000 INFO @ Tue, 16 Jun 2020 08:13:46: 2000000 INFO @ Tue, 16 Jun 2020 08:13:49: 8000000 INFO @ Tue, 16 Jun 2020 08:13:52: 3000000 INFO @ Tue, 16 Jun 2020 08:13:55: 9000000 INFO @ Tue, 16 Jun 2020 08:13:58: 4000000 INFO @ Tue, 16 Jun 2020 08:14:01: 10000000 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 08:14:03: 5000000 INFO @ Tue, 16 Jun 2020 08:14:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.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 08:14:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:06: 11000000 INFO @ Tue, 16 Jun 2020 08:14:09: 6000000 INFO @ Tue, 16 Jun 2020 08:14:11: 1000000 INFO @ Tue, 16 Jun 2020 08:14:13: 12000000 INFO @ Tue, 16 Jun 2020 08:14:15: 7000000 INFO @ Tue, 16 Jun 2020 08:14:17: 2000000 INFO @ Tue, 16 Jun 2020 08:14:19: 13000000 INFO @ Tue, 16 Jun 2020 08:14:21: 8000000 INFO @ Tue, 16 Jun 2020 08:14:23: 3000000 INFO @ Tue, 16 Jun 2020 08:14:25: 14000000 INFO @ Tue, 16 Jun 2020 08:14:27: 9000000 INFO @ Tue, 16 Jun 2020 08:14:29: 4000000 INFO @ Tue, 16 Jun 2020 08:14:31: 15000000 INFO @ Tue, 16 Jun 2020 08:14:34: 10000000 INFO @ Tue, 16 Jun 2020 08:14:35: 5000000 INFO @ Tue, 16 Jun 2020 08:14:37: 16000000 INFO @ Tue, 16 Jun 2020 08:14:40: 11000000 INFO @ Tue, 16 Jun 2020 08:14:40: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:40: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:40: #1 total tags in treatment: 16526367 INFO @ Tue, 16 Jun 2020 08:14:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:40: #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 08:14:41: #1 tags after filtering in treatment: 16526367 INFO @ Tue, 16 Jun 2020 08:14:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:41: 6000000 INFO @ Tue, 16 Jun 2020 08:14:42: #2 number of paired peaks: 916 WARNING @ Tue, 16 Jun 2020 08:14:42: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:42: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:14:42: #2 alternative fragment length(s) may be 4,106 bps INFO @ Tue, 16 Jun 2020 08:14:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.05_model.r INFO @ Tue, 16 Jun 2020 08:14:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:46: 12000000 INFO @ Tue, 16 Jun 2020 08:14:47: 7000000 INFO @ Tue, 16 Jun 2020 08:14:52: 13000000 INFO @ Tue, 16 Jun 2020 08:14:53: 8000000 INFO @ Tue, 16 Jun 2020 08:14:57: 14000000 INFO @ Tue, 16 Jun 2020 08:14:59: 9000000 INFO @ Tue, 16 Jun 2020 08:15:03: 15000000 INFO @ Tue, 16 Jun 2020 08:15:05: 10000000 INFO @ Tue, 16 Jun 2020 08:15:09: 16000000 INFO @ Tue, 16 Jun 2020 08:15:11: 11000000 INFO @ Tue, 16 Jun 2020 08:15:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:12: #1 total tags in treatment: 16526367 INFO @ Tue, 16 Jun 2020 08:15:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:12: #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 08:15:12: #1 tags after filtering in treatment: 16526367 INFO @ Tue, 16 Jun 2020 08:15:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:12: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:14: #2 number of paired peaks: 916 WARNING @ Tue, 16 Jun 2020 08:15:14: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:14: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:14: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:14: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:14: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:14: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:15:14: #2 alternative fragment length(s) may be 4,106 bps INFO @ Tue, 16 Jun 2020 08:15:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.10_model.r INFO @ Tue, 16 Jun 2020 08:15:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:16: 12000000 INFO @ Tue, 16 Jun 2020 08:15:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:22: 13000000 INFO @ Tue, 16 Jun 2020 08:15:28: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:15:33: 15000000 INFO @ Tue, 16 Jun 2020 08:15:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.05_summits.bed INFO @ Tue, 16 Jun 2020 08:15:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8210 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:15:39: 16000000 INFO @ Tue, 16 Jun 2020 08:15:42: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:15:42: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:15:42: #1 total tags in treatment: 16526367 INFO @ Tue, 16 Jun 2020 08:15:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:42: #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 08:15:42: #1 tags after filtering in treatment: 16526367 INFO @ Tue, 16 Jun 2020 08:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:43: #2 number of paired peaks: 916 WARNING @ Tue, 16 Jun 2020 08:15:43: Fewer paired peaks (916) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 916 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:44: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 08:15:44: #2 alternative fragment length(s) may be 4,106 bps INFO @ Tue, 16 Jun 2020 08:15:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.20_model.r INFO @ Tue, 16 Jun 2020 08:15:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.10_summits.bed INFO @ Tue, 16 Jun 2020 08:16:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4078 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2202781/SRX2202781.20_summits.bed INFO @ Tue, 16 Jun 2020 08:16:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1562 records, 4 fields): 4 millis CompletedMACS2peakCalling