Job ID = 6368958 SRX = SRX7635313 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:38:50 prefetch.2.10.7: 1) Downloading 'SRR10969808'... 2020-06-16T00:38:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:37 prefetch.2.10.7: 'SRR10969808' is valid 2020-06-16T00:39:37 prefetch.2.10.7: 1) 'SRR10969808' was downloaded successfully 2020-06-16T00:40:10 prefetch.2.10.7: 'SRR10969808' has 6 unresolved dependencies 2020-06-16T00:40:10 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.5?vdb-ctx=refseq'... 2020-06-16T00:40:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:27 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.5?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:40:27 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.5?vdb-ctx=refseq'... 2020-06-16T00:40:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:43 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:43 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.5?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:40:43 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.4?vdb-ctx=refseq'... 2020-06-16T00:40:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:01 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:01 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.4?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:41:01 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.4?vdb-ctx=refseq'... 2020-06-16T00:41:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:41:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:41:17 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.4?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:41:17 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.5?vdb-ctx=refseq'... 2020-06-16T00:41:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:44:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:44:47 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.5?vdb-ctx=refseq' was downloaded successfully 2020-06-16T00:44:47 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.5?vdb-ctx=refseq'... 2020-06-16T00:44:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:05 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.5?vdb-ctx=refseq' was downloaded successfully Read 14232699 spots for SRR10969808/SRR10969808.sra Written 14232699 spots for SRR10969808/SRR10969808.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: 00:01:48 14232699 reads; of these: 14232699 (100.00%) were unpaired; of these: 6770002 (47.57%) aligned 0 times 6366373 (44.73%) aligned exactly 1 time 1096324 (7.70%) aligned >1 times 52.43% overall alignment rate Time searching: 00:01:48 Overall time: 00:01:48 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_rmdupse_core] 1193368 / 7462697 = 0.1599 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 09:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.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 09:50:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:24: 1000000 INFO @ Tue, 16 Jun 2020 09:50:29: 2000000 INFO @ Tue, 16 Jun 2020 09:50:34: 3000000 INFO @ Tue, 16 Jun 2020 09:50:40: 4000000 INFO @ Tue, 16 Jun 2020 09:50:45: 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 09:50:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.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 09:50:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:51: 6000000 INFO @ Tue, 16 Jun 2020 09:50:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:52: #1 total tags in treatment: 6269329 INFO @ Tue, 16 Jun 2020 09:50:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:52: #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 09:50:52: #1 tags after filtering in treatment: 6269329 INFO @ Tue, 16 Jun 2020 09:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 09:50:53: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:53: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 09:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.05_model.r INFO @ Tue, 16 Jun 2020 09:50:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:54: 1000000 INFO @ Tue, 16 Jun 2020 09:51:00: 2000000 INFO @ Tue, 16 Jun 2020 09:51:05: 3000000 INFO @ Tue, 16 Jun 2020 09:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:10: 4000000 INFO @ Tue, 16 Jun 2020 09:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4144 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:16: 5000000 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 09:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.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 09:51:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:21: 6000000 INFO @ Tue, 16 Jun 2020 09:51:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:23: #1 total tags in treatment: 6269329 INFO @ Tue, 16 Jun 2020 09:51:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:23: #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 09:51:23: #1 tags after filtering in treatment: 6269329 INFO @ Tue, 16 Jun 2020 09:51:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:23: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 09:51:23: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:23: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:51:23: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 09:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.10_model.r INFO @ Tue, 16 Jun 2020 09:51:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:24: 1000000 INFO @ Tue, 16 Jun 2020 09:51:29: 2000000 INFO @ Tue, 16 Jun 2020 09:51:35: 3000000 INFO @ Tue, 16 Jun 2020 09:51:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:40: 4000000 INFO @ Tue, 16 Jun 2020 09:51:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2315 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:45: 5000000 INFO @ Tue, 16 Jun 2020 09:51:51: 6000000 INFO @ Tue, 16 Jun 2020 09:51:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:52: #1 total tags in treatment: 6269329 INFO @ Tue, 16 Jun 2020 09:51:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:52: #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 09:51:52: #1 tags after filtering in treatment: 6269329 INFO @ Tue, 16 Jun 2020 09:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:52: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:53: #2 number of paired peaks: 784 WARNING @ Tue, 16 Jun 2020 09:51:53: Fewer paired peaks (784) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 784 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:53: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:51:53: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 09:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.20_model.r INFO @ Tue, 16 Jun 2020 09:51:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7635313/SRX7635313.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 2 millis CompletedMACS2peakCalling