Job ID = 12266653 SRX = SRX7806725 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12073338 spots for SRR11186391/SRR11186391.sra Written 12073338 spots for SRR11186391/SRR11186391.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266956 ("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: 00:20:35 12073338 reads; of these: 12073338 (100.00%) were paired; of these: 5687610 (47.11%) aligned concordantly 0 times 4546668 (37.66%) aligned concordantly exactly 1 time 1839060 (15.23%) aligned concordantly >1 times ---- 5687610 pairs aligned concordantly 0 times; of these: 1095146 (19.25%) aligned discordantly 1 time ---- 4592464 pairs aligned 0 times concordantly or discordantly; of these: 9184928 mates make up the pairs; of these: 7966714 (86.74%) aligned 0 times 586220 (6.38%) aligned exactly 1 time 631994 (6.88%) aligned >1 times 67.01% overall alignment rate Time searching: 00:20:35 Overall time: 00:20:35 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_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 941124 / 7436650 = 0.1266 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:31:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.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 @ Sat, 03 Apr 2021 09:31:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:31:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:31:13: 1000000 INFO @ Sat, 03 Apr 2021 09:31:18: 2000000 INFO @ Sat, 03 Apr 2021 09:31:24: 3000000 INFO @ Sat, 03 Apr 2021 09:31:29: 4000000 INFO @ Sat, 03 Apr 2021 09:31:34: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.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 @ Sat, 03 Apr 2021 09:31:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:31:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:31:40: 6000000 INFO @ Sat, 03 Apr 2021 09:31:43: 1000000 INFO @ Sat, 03 Apr 2021 09:31:45: 7000000 INFO @ Sat, 03 Apr 2021 09:31:48: 2000000 INFO @ Sat, 03 Apr 2021 09:31:50: 8000000 INFO @ Sat, 03 Apr 2021 09:31:54: 3000000 INFO @ Sat, 03 Apr 2021 09:31:56: 9000000 INFO @ Sat, 03 Apr 2021 09:31:59: 4000000 INFO @ Sat, 03 Apr 2021 09:32:01: 10000000 INFO @ Sat, 03 Apr 2021 09:32:05: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:32:07: 11000000 INFO @ Sat, 03 Apr 2021 09:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.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 @ Sat, 03 Apr 2021 09:32:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:32:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:32:10: 6000000 INFO @ Sat, 03 Apr 2021 09:32:12: 12000000 INFO @ Sat, 03 Apr 2021 09:32:14: 1000000 INFO @ Sat, 03 Apr 2021 09:32:16: 7000000 INFO @ Sat, 03 Apr 2021 09:32:18: 13000000 INFO @ Sat, 03 Apr 2021 09:32:20: 2000000 INFO @ Sat, 03 Apr 2021 09:32:21: 8000000 INFO @ Sat, 03 Apr 2021 09:32:24: 14000000 INFO @ Sat, 03 Apr 2021 09:32:25: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:32:25: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:32:25: #1 total tags in treatment: 5505928 INFO @ Sat, 03 Apr 2021 09:32:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:32:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:32:26: #1 tags after filtering in treatment: 4594639 INFO @ Sat, 03 Apr 2021 09:32:26: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 09:32:26: #1 finished! INFO @ Sat, 03 Apr 2021 09:32:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:32:26: #2 number of paired peaks: 2117 INFO @ Sat, 03 Apr 2021 09:32:26: start model_add_line... INFO @ Sat, 03 Apr 2021 09:32:26: start X-correlation... INFO @ Sat, 03 Apr 2021 09:32:26: end of X-cor INFO @ Sat, 03 Apr 2021 09:32:26: #2 finished! INFO @ Sat, 03 Apr 2021 09:32:26: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 09:32:26: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 03 Apr 2021 09:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.05_model.r INFO @ Sat, 03 Apr 2021 09:32:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:32:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:32:26: 3000000 INFO @ Sat, 03 Apr 2021 09:32:27: 9000000 INFO @ Sat, 03 Apr 2021 09:32:33: 10000000 INFO @ Sat, 03 Apr 2021 09:32:33: 4000000 INFO @ Sat, 03 Apr 2021 09:32:38: 11000000 INFO @ Sat, 03 Apr 2021 09:32:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:32:39: 5000000 INFO @ Sat, 03 Apr 2021 09:32:43: 12000000 INFO @ Sat, 03 Apr 2021 09:32:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:32:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:32:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.05_summits.bed INFO @ Sat, 03 Apr 2021 09:32:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6894 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:32:46: 6000000 INFO @ Sat, 03 Apr 2021 09:32:49: 13000000 INFO @ Sat, 03 Apr 2021 09:32:52: 7000000 INFO @ Sat, 03 Apr 2021 09:32:55: 14000000 INFO @ Sat, 03 Apr 2021 09:32:56: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:32:56: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:32:56: #1 total tags in treatment: 5505928 INFO @ Sat, 03 Apr 2021 09:32:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:32:57: #1 tags after filtering in treatment: 4594639 INFO @ Sat, 03 Apr 2021 09:32:57: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 09:32:57: #1 finished! INFO @ Sat, 03 Apr 2021 09:32:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:32:57: #2 number of paired peaks: 2117 INFO @ Sat, 03 Apr 2021 09:32:57: start model_add_line... INFO @ Sat, 03 Apr 2021 09:32:57: start X-correlation... INFO @ Sat, 03 Apr 2021 09:32:57: end of X-cor INFO @ Sat, 03 Apr 2021 09:32:57: #2 finished! INFO @ Sat, 03 Apr 2021 09:32:57: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 09:32:57: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 03 Apr 2021 09:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.10_model.r INFO @ Sat, 03 Apr 2021 09:32:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:32:58: 8000000 INFO @ Sat, 03 Apr 2021 09:33:04: 9000000 INFO @ Sat, 03 Apr 2021 09:33:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:33:11: 10000000 INFO @ Sat, 03 Apr 2021 09:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.10_summits.bed INFO @ Sat, 03 Apr 2021 09:33:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3253 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:33:17: 11000000 INFO @ Sat, 03 Apr 2021 09:33:23: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:33:29: 13000000 INFO @ Sat, 03 Apr 2021 09:33:36: 14000000 INFO @ Sat, 03 Apr 2021 09:33:38: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:33:38: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:33:38: #1 total tags in treatment: 5505928 INFO @ Sat, 03 Apr 2021 09:33:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:33:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:33:38: #1 tags after filtering in treatment: 4594639 INFO @ Sat, 03 Apr 2021 09:33:38: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 03 Apr 2021 09:33:38: #1 finished! INFO @ Sat, 03 Apr 2021 09:33:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:33:38: #2 number of paired peaks: 2117 INFO @ Sat, 03 Apr 2021 09:33:38: start model_add_line... INFO @ Sat, 03 Apr 2021 09:33:38: start X-correlation... INFO @ Sat, 03 Apr 2021 09:33:38: end of X-cor INFO @ Sat, 03 Apr 2021 09:33:38: #2 finished! INFO @ Sat, 03 Apr 2021 09:33:38: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Apr 2021 09:33:38: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 03 Apr 2021 09:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.20_model.r INFO @ Sat, 03 Apr 2021 09:33:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:33:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806725/SRX7806725.20_summits.bed INFO @ Sat, 03 Apr 2021 09:33:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (927 records, 4 fields): 4 millis CompletedMACS2peakCalling