Job ID = 6365908 SRX = SRX027210 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:30:44 prefetch.2.10.7: 1) Downloading 'SRR066593'... 2020-06-15T22:30:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:32:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:32:36 prefetch.2.10.7: 'SRR066593' is valid 2020-06-15T22:32:36 prefetch.2.10.7: 1) 'SRR066593' was downloaded successfully Read 21006018 spots for SRR066593/SRR066593.sra Written 21006018 spots for SRR066593/SRR066593.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: 00:02:42 21006018 reads; of these: 21006018 (100.00%) were unpaired; of these: 7276905 (34.64%) aligned 0 times 12187981 (58.02%) aligned exactly 1 time 1541132 (7.34%) aligned >1 times 65.36% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 3460327 / 13729113 = 0.2520 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 07:39:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.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 07:39:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:27: 1000000 INFO @ Tue, 16 Jun 2020 07:39:32: 2000000 INFO @ Tue, 16 Jun 2020 07:39:37: 3000000 INFO @ Tue, 16 Jun 2020 07:39:42: 4000000 INFO @ Tue, 16 Jun 2020 07:39:47: 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 07:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.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 07:39:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:39:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:39:53: 6000000 INFO @ Tue, 16 Jun 2020 07:39:58: 1000000 INFO @ Tue, 16 Jun 2020 07:39:59: 7000000 INFO @ Tue, 16 Jun 2020 07:40:04: 2000000 INFO @ Tue, 16 Jun 2020 07:40:05: 8000000 INFO @ Tue, 16 Jun 2020 07:40:11: 9000000 INFO @ Tue, 16 Jun 2020 07:40:11: 3000000 INFO @ Tue, 16 Jun 2020 07:40:16: 10000000 INFO @ Tue, 16 Jun 2020 07:40:17: 4000000 INFO @ Tue, 16 Jun 2020 07:40:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:18: #1 total tags in treatment: 10268786 INFO @ Tue, 16 Jun 2020 07:40:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:18: #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 07:40:18: #1 tags after filtering in treatment: 10268786 INFO @ Tue, 16 Jun 2020 07:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:40:19: #2 number of paired peaks: 3989 INFO @ Tue, 16 Jun 2020 07:40:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:40:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:40:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:40:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:40:19: #2 predicted fragment length is 234 bps INFO @ Tue, 16 Jun 2020 07:40:19: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 16 Jun 2020 07:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.05_model.r INFO @ Tue, 16 Jun 2020 07:40:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:40:19: #3 Pre-compute pvalue-qvalue table... 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 07:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.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 07:40:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:40:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:40:24: 5000000 INFO @ Tue, 16 Jun 2020 07:40:27: 1000000 INFO @ Tue, 16 Jun 2020 07:40:30: 6000000 INFO @ Tue, 16 Jun 2020 07:40:33: 2000000 INFO @ Tue, 16 Jun 2020 07:40:37: 7000000 INFO @ Tue, 16 Jun 2020 07:40:39: 3000000 INFO @ Tue, 16 Jun 2020 07:40:44: 8000000 INFO @ Tue, 16 Jun 2020 07:40:45: 4000000 INFO @ Tue, 16 Jun 2020 07:40:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:40:50: 9000000 INFO @ Tue, 16 Jun 2020 07:40:50: 5000000 INFO @ Tue, 16 Jun 2020 07:40:56: 6000000 INFO @ Tue, 16 Jun 2020 07:40:57: 10000000 INFO @ Tue, 16 Jun 2020 07:40:58: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:40:58: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:40:58: #1 total tags in treatment: 10268786 INFO @ Tue, 16 Jun 2020 07:40:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:40:58: #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 07:40:59: #1 tags after filtering in treatment: 10268786 INFO @ Tue, 16 Jun 2020 07:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:40:59: #1 finished! INFO @ Tue, 16 Jun 2020 07:40:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:00: #2 number of paired peaks: 3989 INFO @ Tue, 16 Jun 2020 07:41:00: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:00: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:00: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:00: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:00: #2 predicted fragment length is 234 bps INFO @ Tue, 16 Jun 2020 07:41:00: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 16 Jun 2020 07:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.10_model.r INFO @ Tue, 16 Jun 2020 07:41:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:02: 7000000 INFO @ Tue, 16 Jun 2020 07:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5242 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:41:07: 8000000 INFO @ Tue, 16 Jun 2020 07:41:12: 9000000 INFO @ Tue, 16 Jun 2020 07:41:17: 10000000 INFO @ Tue, 16 Jun 2020 07:41:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:41:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:41:18: #1 total tags in treatment: 10268786 INFO @ Tue, 16 Jun 2020 07:41:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:18: #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 07:41:19: #1 tags after filtering in treatment: 10268786 INFO @ Tue, 16 Jun 2020 07:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:20: #2 number of paired peaks: 3989 INFO @ Tue, 16 Jun 2020 07:41:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:20: #2 predicted fragment length is 234 bps INFO @ Tue, 16 Jun 2020 07:41:20: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 16 Jun 2020 07:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.20_model.r INFO @ Tue, 16 Jun 2020 07:41:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:41:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.10_summits.bed INFO @ Tue, 16 Jun 2020 07:41:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4291 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:41:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX027210/SRX027210.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3511 records, 4 fields): 5 millis CompletedMACS2peakCalling