Job ID = 6365981 SRX = SRX043992 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:27:44 prefetch.2.10.7: 1) Downloading 'SRR107568'... 2020-06-15T22:27:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:28:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:28:05 prefetch.2.10.7: 'SRR107568' is valid 2020-06-15T22:28:05 prefetch.2.10.7: 1) 'SRR107568' was downloaded successfully Read 3277607 spots for SRR107568/SRR107568.sra Written 3277607 spots for SRR107568/SRR107568.sra 2020-06-15T22:28:26 prefetch.2.10.7: 1) Downloading 'SRR107569'... 2020-06-15T22:28:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:29:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:29:01 prefetch.2.10.7: 'SRR107569' is valid 2020-06-15T22:29:01 prefetch.2.10.7: 1) 'SRR107569' was downloaded successfully Read 3599838 spots for SRR107569/SRR107569.sra Written 3599838 spots for SRR107569/SRR107569.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: 00:01:05 6877445 reads; of these: 6877445 (100.00%) were unpaired; of these: 364132 (5.29%) aligned 0 times 5724261 (83.23%) aligned exactly 1 time 789052 (11.47%) aligned >1 times 94.71% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 1032505 / 6513313 = 0.1585 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 07:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.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 07:32:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:28: 1000000 INFO @ Tue, 16 Jun 2020 07:32:34: 2000000 INFO @ Tue, 16 Jun 2020 07:32:41: 3000000 INFO @ Tue, 16 Jun 2020 07:32:47: 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 07:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.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 07:32:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:32:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:32:54: 5000000 INFO @ Tue, 16 Jun 2020 07:32:57: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:32:57: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:32:57: #1 total tags in treatment: 5480808 INFO @ Tue, 16 Jun 2020 07:32:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:32:57: #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 07:32:57: #1 tags after filtering in treatment: 5480808 INFO @ Tue, 16 Jun 2020 07:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:32:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:32:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:32:57: #2 number of paired peaks: 1442 INFO @ Tue, 16 Jun 2020 07:32:57: start model_add_line... INFO @ Tue, 16 Jun 2020 07:32:57: start X-correlation... INFO @ Tue, 16 Jun 2020 07:32:57: end of X-cor INFO @ Tue, 16 Jun 2020 07:32:57: #2 finished! INFO @ Tue, 16 Jun 2020 07:32:57: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:32:57: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 07:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.05_model.r INFO @ Tue, 16 Jun 2020 07:32:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:32:59: 1000000 INFO @ Tue, 16 Jun 2020 07:33:05: 2000000 INFO @ Tue, 16 Jun 2020 07:33:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:12: 3000000 INFO @ Tue, 16 Jun 2020 07:33:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.05_summits.bed INFO @ Tue, 16 Jun 2020 07:33:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7430 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:33:18: 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 @ Tue, 16 Jun 2020 07:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.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 07:33:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:33:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:33:25: 5000000 INFO @ Tue, 16 Jun 2020 07:33:28: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:33:28: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:33:28: #1 total tags in treatment: 5480808 INFO @ Tue, 16 Jun 2020 07:33:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:28: #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 07:33:28: #1 tags after filtering in treatment: 5480808 INFO @ Tue, 16 Jun 2020 07:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:28: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:28: #2 number of paired peaks: 1442 INFO @ Tue, 16 Jun 2020 07:33:28: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:29: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:29: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:29: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:29: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:33:29: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 07:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.10_model.r INFO @ Tue, 16 Jun 2020 07:33:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:33:29: 1000000 INFO @ Tue, 16 Jun 2020 07:33:35: 2000000 INFO @ Tue, 16 Jun 2020 07:33:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:33:42: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:33:49: 4000000 INFO @ Tue, 16 Jun 2020 07:33:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:33:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:33:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.10_summits.bed INFO @ Tue, 16 Jun 2020 07:33:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4960 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:33:55: 5000000 INFO @ Tue, 16 Jun 2020 07:33:58: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:33:58: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:33:58: #1 total tags in treatment: 5480808 INFO @ Tue, 16 Jun 2020 07:33:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:58: #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 07:33:58: #1 tags after filtering in treatment: 5480808 INFO @ Tue, 16 Jun 2020 07:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:58: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:33:59: #2 number of paired peaks: 1442 INFO @ Tue, 16 Jun 2020 07:33:59: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:59: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:59: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:59: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:59: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:33:59: #2 alternative fragment length(s) may be 137 bps INFO @ Tue, 16 Jun 2020 07:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.20_model.r INFO @ Tue, 16 Jun 2020 07:33:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043992/SRX043992.20_summits.bed INFO @ Tue, 16 Jun 2020 07:34:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2439 records, 4 fields): 4 millis CompletedMACS2peakCalling