Job ID = 14171783 SRX = SRX9008832 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14879452 spots for SRR12518304/SRR12518304.sra Written 14879452 spots for SRR12518304/SRR12518304.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172281 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:20 14879452 reads; of these: 14879452 (100.00%) were paired; of these: 1467726 (9.86%) aligned concordantly 0 times 11580187 (77.83%) aligned concordantly exactly 1 time 1831539 (12.31%) aligned concordantly >1 times ---- 1467726 pairs aligned concordantly 0 times; of these: 178727 (12.18%) aligned discordantly 1 time ---- 1288999 pairs aligned 0 times concordantly or discordantly; of these: 2577998 mates make up the pairs; of these: 2024768 (78.54%) aligned 0 times 373345 (14.48%) aligned exactly 1 time 179885 (6.98%) aligned >1 times 93.20% overall alignment rate Time searching: 00:20:21 Overall time: 00:20:21 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 12 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] 1051470 / 13562042 = 0.0775 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.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, 11 Dec 2021 13:18:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:18:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:18:52: 1000000 INFO @ Sat, 11 Dec 2021 13:18:57: 2000000 INFO @ Sat, 11 Dec 2021 13:19:02: 3000000 INFO @ Sat, 11 Dec 2021 13:19:08: 4000000 INFO @ Sat, 11 Dec 2021 13:19:13: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.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, 11 Dec 2021 13:19:16: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:19:16: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:19:20: 6000000 INFO @ Sat, 11 Dec 2021 13:19:23: 1000000 INFO @ Sat, 11 Dec 2021 13:19:26: 7000000 INFO @ Sat, 11 Dec 2021 13:19:30: 2000000 INFO @ Sat, 11 Dec 2021 13:19:32: 8000000 INFO @ Sat, 11 Dec 2021 13:19:37: 3000000 INFO @ Sat, 11 Dec 2021 13:19:39: 9000000 INFO @ Sat, 11 Dec 2021 13:19:44: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 13:19:45: 10000000 INFO @ Sat, 11 Dec 2021 13:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.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, 11 Dec 2021 13:19:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:19:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:19:51: 5000000 INFO @ Sat, 11 Dec 2021 13:19:52: 11000000 INFO @ Sat, 11 Dec 2021 13:19:53: 1000000 INFO @ Sat, 11 Dec 2021 13:19:58: 12000000 INFO @ Sat, 11 Dec 2021 13:19:58: 6000000 INFO @ Sat, 11 Dec 2021 13:19:59: 2000000 INFO @ Sat, 11 Dec 2021 13:20:04: 13000000 INFO @ Sat, 11 Dec 2021 13:20:05: 7000000 INFO @ Sat, 11 Dec 2021 13:20:06: 3000000 INFO @ Sat, 11 Dec 2021 13:20:11: 14000000 INFO @ Sat, 11 Dec 2021 13:20:12: 8000000 INFO @ Sat, 11 Dec 2021 13:20:12: 4000000 INFO @ Sat, 11 Dec 2021 13:20:17: 15000000 INFO @ Sat, 11 Dec 2021 13:20:19: 5000000 INFO @ Sat, 11 Dec 2021 13:20:19: 9000000 INFO @ Sat, 11 Dec 2021 13:20:24: 16000000 INFO @ Sat, 11 Dec 2021 13:20:25: 6000000 INFO @ Sat, 11 Dec 2021 13:20:26: 10000000 INFO @ Sat, 11 Dec 2021 13:20:30: 17000000 INFO @ Sat, 11 Dec 2021 13:20:32: 7000000 INFO @ Sat, 11 Dec 2021 13:20:33: 11000000 INFO @ Sat, 11 Dec 2021 13:20:37: 18000000 INFO @ Sat, 11 Dec 2021 13:20:38: 8000000 INFO @ Sat, 11 Dec 2021 13:20:40: 12000000 INFO @ Sat, 11 Dec 2021 13:20:43: 19000000 INFO @ Sat, 11 Dec 2021 13:20:45: 9000000 INFO @ Sat, 11 Dec 2021 13:20:47: 13000000 INFO @ Sat, 11 Dec 2021 13:20:50: 20000000 INFO @ Sat, 11 Dec 2021 13:20:51: 10000000 INFO @ Sat, 11 Dec 2021 13:20:54: 14000000 INFO @ Sat, 11 Dec 2021 13:20:56: 21000000 INFO @ Sat, 11 Dec 2021 13:20:58: 11000000 INFO @ Sat, 11 Dec 2021 13:21:01: 15000000 INFO @ Sat, 11 Dec 2021 13:21:03: 22000000 INFO @ Sat, 11 Dec 2021 13:21:04: 12000000 INFO @ Sat, 11 Dec 2021 13:21:07: 16000000 INFO @ Sat, 11 Dec 2021 13:21:09: 23000000 INFO @ Sat, 11 Dec 2021 13:21:10: 13000000 INFO @ Sat, 11 Dec 2021 13:21:14: 17000000 INFO @ Sat, 11 Dec 2021 13:21:16: 24000000 INFO @ Sat, 11 Dec 2021 13:21:17: 14000000 INFO @ Sat, 11 Dec 2021 13:21:21: 18000000 INFO @ Sat, 11 Dec 2021 13:21:22: 25000000 INFO @ Sat, 11 Dec 2021 13:21:23: 15000000 INFO @ Sat, 11 Dec 2021 13:21:26: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 13:21:26: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 13:21:26: #1 total tags in treatment: 12364618 INFO @ Sat, 11 Dec 2021 13:21:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:21:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:21:27: #1 tags after filtering in treatment: 11754195 INFO @ Sat, 11 Dec 2021 13:21:27: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:21:27: #1 finished! INFO @ Sat, 11 Dec 2021 13:21:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:21:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:21:27: #2 number of paired peaks: 977 WARNING @ Sat, 11 Dec 2021 13:21:27: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sat, 11 Dec 2021 13:21:27: start model_add_line... INFO @ Sat, 11 Dec 2021 13:21:27: start X-correlation... INFO @ Sat, 11 Dec 2021 13:21:27: end of X-cor INFO @ Sat, 11 Dec 2021 13:21:27: #2 finished! INFO @ Sat, 11 Dec 2021 13:21:27: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 13:21:27: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 13:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.05_model.r INFO @ Sat, 11 Dec 2021 13:21:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:21:28: 19000000 INFO @ Sat, 11 Dec 2021 13:21:30: 16000000 INFO @ Sat, 11 Dec 2021 13:21:35: 20000000 INFO @ Sat, 11 Dec 2021 13:21:36: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:21:42: 18000000 INFO @ Sat, 11 Dec 2021 13:21:43: 21000000 INFO @ Sat, 11 Dec 2021 13:21:49: 19000000 INFO @ Sat, 11 Dec 2021 13:21:50: 22000000 INFO @ Sat, 11 Dec 2021 13:21:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:21:55: 20000000 INFO @ Sat, 11 Dec 2021 13:21:57: 23000000 INFO @ Sat, 11 Dec 2021 13:22:02: 21000000 INFO @ Sat, 11 Dec 2021 13:22:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:22:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:22:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.05_summits.bed INFO @ Sat, 11 Dec 2021 13:22:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5048 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:22:04: 24000000 INFO @ Sat, 11 Dec 2021 13:22:08: 22000000 INFO @ Sat, 11 Dec 2021 13:22:11: 25000000 INFO @ Sat, 11 Dec 2021 13:22:14: 23000000 INFO @ Sat, 11 Dec 2021 13:22:15: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 13:22:15: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 13:22:15: #1 total tags in treatment: 12364618 INFO @ Sat, 11 Dec 2021 13:22:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:22:15: #1 tags after filtering in treatment: 11754195 INFO @ Sat, 11 Dec 2021 13:22:15: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:22:15: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:16: #2 number of paired peaks: 977 WARNING @ Sat, 11 Dec 2021 13:22:16: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:16: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:16: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:16: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:16: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:16: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 13:22:16: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 13:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.10_model.r INFO @ Sat, 11 Dec 2021 13:22:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:22:20: 24000000 INFO @ Sat, 11 Dec 2021 13:22:26: 25000000 INFO @ Sat, 11 Dec 2021 13:22:29: #1 tag size is determined as 75 bps INFO @ Sat, 11 Dec 2021 13:22:29: #1 tag size = 75 INFO @ Sat, 11 Dec 2021 13:22:29: #1 total tags in treatment: 12364618 INFO @ Sat, 11 Dec 2021 13:22:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:22:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:22:29: #1 tags after filtering in treatment: 11754195 INFO @ Sat, 11 Dec 2021 13:22:29: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 13:22:29: #1 finished! INFO @ Sat, 11 Dec 2021 13:22:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:22:30: #2 number of paired peaks: 977 WARNING @ Sat, 11 Dec 2021 13:22:30: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sat, 11 Dec 2021 13:22:30: start model_add_line... INFO @ Sat, 11 Dec 2021 13:22:30: start X-correlation... INFO @ Sat, 11 Dec 2021 13:22:30: end of X-cor INFO @ Sat, 11 Dec 2021 13:22:30: #2 finished! INFO @ Sat, 11 Dec 2021 13:22:30: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 13:22:30: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 13:22:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.20_model.r INFO @ Sat, 11 Dec 2021 13:22:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:22:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:22:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:22:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:22:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:22:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.10_summits.bed INFO @ Sat, 11 Dec 2021 13:22:53: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3953 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:22:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:23:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008832/SRX9008832.20_summits.bed INFO @ Sat, 11 Dec 2021 13:23:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2417 records, 4 fields): 4 millis CompletedMACS2peakCalling