Job ID = 6626553 SRX = SRX6813090 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10715840 spots for SRR10080052/SRR10080052.sra Written 10715840 spots for SRR10080052/SRR10080052.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626680 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:02 10715840 reads; of these: 10715840 (100.00%) were unpaired; of these: 3325909 (31.04%) aligned 0 times 6628094 (61.85%) aligned exactly 1 time 761837 (7.11%) aligned >1 times 68.96% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 839892 / 7389931 = 0.1137 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, 14 Jul 2020 07:35:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 07:35:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:35:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:35:45: 1000000 INFO @ Tue, 14 Jul 2020 07:35:51: 2000000 INFO @ Tue, 14 Jul 2020 07:35:57: 3000000 INFO @ Tue, 14 Jul 2020 07:36:03: 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, 14 Jul 2020 07:36:09: 5000000 INFO @ Tue, 14 Jul 2020 07:36:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 07:36:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:15: 6000000 INFO @ Tue, 14 Jul 2020 07:36:16: 1000000 INFO @ Tue, 14 Jul 2020 07:36:18: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:18: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:18: #1 total tags in treatment: 6550039 INFO @ Tue, 14 Jul 2020 07:36:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:36:18: #1 tags after filtering in treatment: 6550039 INFO @ Tue, 14 Jul 2020 07:36:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:18: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:19: #2 number of paired peaks: 9070 INFO @ Tue, 14 Jul 2020 07:36:19: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:19: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:19: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:19: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:19: #2 predicted fragment length is 234 bps INFO @ Tue, 14 Jul 2020 07:36:19: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 14 Jul 2020 07:36:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.05_model.r INFO @ Tue, 14 Jul 2020 07:36:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:22: 2000000 INFO @ Tue, 14 Jul 2020 07:36:28: 3000000 INFO @ Tue, 14 Jul 2020 07:36:34: 4000000 INFO @ Tue, 14 Jul 2020 07:36:37: #3 Call peaks for each chromosome... 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, 14 Jul 2020 07:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 07:36:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:36:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:36:40: 5000000 INFO @ Tue, 14 Jul 2020 07:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:36:46: 1000000 INFO @ Tue, 14 Jul 2020 07:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:36:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.05_summits.bed INFO @ Tue, 14 Jul 2020 07:36:46: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7482 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:36:47: 6000000 INFO @ Tue, 14 Jul 2020 07:36:50: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:36:50: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:36:50: #1 total tags in treatment: 6550039 INFO @ Tue, 14 Jul 2020 07:36:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:36:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:36:50: #1 tags after filtering in treatment: 6550039 INFO @ Tue, 14 Jul 2020 07:36:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:36:50: #1 finished! INFO @ Tue, 14 Jul 2020 07:36:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:36:51: #2 number of paired peaks: 9070 INFO @ Tue, 14 Jul 2020 07:36:51: start model_add_line... INFO @ Tue, 14 Jul 2020 07:36:51: start X-correlation... INFO @ Tue, 14 Jul 2020 07:36:51: end of X-cor INFO @ Tue, 14 Jul 2020 07:36:51: #2 finished! INFO @ Tue, 14 Jul 2020 07:36:51: #2 predicted fragment length is 234 bps INFO @ Tue, 14 Jul 2020 07:36:51: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 14 Jul 2020 07:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.10_model.r INFO @ Tue, 14 Jul 2020 07:36:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:36:52: 2000000 INFO @ Tue, 14 Jul 2020 07:36:58: 3000000 INFO @ Tue, 14 Jul 2020 07:37:04: 4000000 INFO @ Tue, 14 Jul 2020 07:37:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:10: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:37:17: 6000000 INFO @ Tue, 14 Jul 2020 07:37:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.10_summits.bed INFO @ Tue, 14 Jul 2020 07:37:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5037 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:37:20: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 07:37:20: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 07:37:20: #1 total tags in treatment: 6550039 INFO @ Tue, 14 Jul 2020 07:37:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:37:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:37:20: #1 tags after filtering in treatment: 6550039 INFO @ Tue, 14 Jul 2020 07:37:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:37:20: #1 finished! INFO @ Tue, 14 Jul 2020 07:37:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:37:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:37:21: #2 number of paired peaks: 9070 INFO @ Tue, 14 Jul 2020 07:37:21: start model_add_line... INFO @ Tue, 14 Jul 2020 07:37:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:37:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:37:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:37:21: #2 predicted fragment length is 234 bps INFO @ Tue, 14 Jul 2020 07:37:21: #2 alternative fragment length(s) may be 234 bps INFO @ Tue, 14 Jul 2020 07:37:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.20_model.r INFO @ Tue, 14 Jul 2020 07:37:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:37:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:37:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6813090/SRX6813090.20_summits.bed INFO @ Tue, 14 Jul 2020 07:37:49: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2246 records, 4 fields): 4 millis CompletedMACS2peakCalling