Job ID = 6626522 SRX = SRX5736496 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12637403 spots for SRR8956907/SRR8956907.sra Written 12637403 spots for SRR8956907/SRR8956907.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626733 ("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: 00:35:38 12637403 reads; of these: 12637403 (100.00%) were paired; of these: 1687226 (13.35%) aligned concordantly 0 times 6853655 (54.23%) aligned concordantly exactly 1 time 4096522 (32.42%) aligned concordantly >1 times ---- 1687226 pairs aligned concordantly 0 times; of these: 371210 (22.00%) aligned discordantly 1 time ---- 1316016 pairs aligned 0 times concordantly or discordantly; of these: 2632032 mates make up the pairs; of these: 1579739 (60.02%) aligned 0 times 402233 (15.28%) aligned exactly 1 time 650060 (24.70%) aligned >1 times 93.75% overall alignment rate Time searching: 00:35:38 Overall time: 00:35:38 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] 444368 / 11297939 = 0.0393 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 08:02:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.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 08:02:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:02:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:02:36: 1000000 INFO @ Tue, 14 Jul 2020 08:02:41: 2000000 INFO @ Tue, 14 Jul 2020 08:02:47: 3000000 INFO @ Tue, 14 Jul 2020 08:02:52: 4000000 INFO @ Tue, 14 Jul 2020 08:02:58: 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, 14 Jul 2020 08:03:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.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 08:03:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:03:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:03:03: 6000000 INFO @ Tue, 14 Jul 2020 08:03:07: 1000000 INFO @ Tue, 14 Jul 2020 08:03:09: 7000000 INFO @ Tue, 14 Jul 2020 08:03:14: 2000000 INFO @ Tue, 14 Jul 2020 08:03:15: 8000000 INFO @ Tue, 14 Jul 2020 08:03:20: 3000000 INFO @ Tue, 14 Jul 2020 08:03:21: 9000000 INFO @ Tue, 14 Jul 2020 08:03:26: 10000000 INFO @ Tue, 14 Jul 2020 08:03:27: 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, 14 Jul 2020 08:03:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.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 08:03:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:03:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:03:32: 11000000 INFO @ Tue, 14 Jul 2020 08:03:34: 5000000 INFO @ Tue, 14 Jul 2020 08:03:37: 1000000 INFO @ Tue, 14 Jul 2020 08:03:38: 12000000 INFO @ Tue, 14 Jul 2020 08:03:41: 6000000 INFO @ Tue, 14 Jul 2020 08:03:44: 13000000 INFO @ Tue, 14 Jul 2020 08:03:45: 2000000 INFO @ Tue, 14 Jul 2020 08:03:48: 7000000 INFO @ Tue, 14 Jul 2020 08:03:50: 14000000 INFO @ Tue, 14 Jul 2020 08:03:52: 3000000 INFO @ Tue, 14 Jul 2020 08:03:55: 8000000 INFO @ Tue, 14 Jul 2020 08:03:55: 15000000 INFO @ Tue, 14 Jul 2020 08:03:58: 4000000 INFO @ Tue, 14 Jul 2020 08:04:01: 16000000 INFO @ Tue, 14 Jul 2020 08:04:02: 9000000 INFO @ Tue, 14 Jul 2020 08:04:05: 5000000 INFO @ Tue, 14 Jul 2020 08:04:07: 17000000 INFO @ Tue, 14 Jul 2020 08:04:09: 10000000 INFO @ Tue, 14 Jul 2020 08:04:13: 18000000 INFO @ Tue, 14 Jul 2020 08:04:13: 6000000 INFO @ Tue, 14 Jul 2020 08:04:16: 11000000 INFO @ Tue, 14 Jul 2020 08:04:19: 19000000 INFO @ Tue, 14 Jul 2020 08:04:21: 7000000 INFO @ Tue, 14 Jul 2020 08:04:23: 12000000 INFO @ Tue, 14 Jul 2020 08:04:25: 20000000 INFO @ Tue, 14 Jul 2020 08:04:28: 8000000 INFO @ Tue, 14 Jul 2020 08:04:30: 13000000 INFO @ Tue, 14 Jul 2020 08:04:31: 21000000 INFO @ Tue, 14 Jul 2020 08:04:35: 9000000 INFO @ Tue, 14 Jul 2020 08:04:36: 22000000 INFO @ Tue, 14 Jul 2020 08:04:37: 14000000 INFO @ Tue, 14 Jul 2020 08:04:41: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:04:41: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:04:41: #1 total tags in treatment: 10514604 INFO @ Tue, 14 Jul 2020 08:04:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:04:41: #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 08:04:41: #1 tags after filtering in treatment: 9593563 INFO @ Tue, 14 Jul 2020 08:04:41: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:04:41: #1 finished! INFO @ Tue, 14 Jul 2020 08:04:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:04:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:04:42: #2 number of paired peaks: 357 WARNING @ Tue, 14 Jul 2020 08:04:42: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 14 Jul 2020 08:04:42: start model_add_line... INFO @ Tue, 14 Jul 2020 08:04:42: start X-correlation... INFO @ Tue, 14 Jul 2020 08:04:42: end of X-cor INFO @ Tue, 14 Jul 2020 08:04:42: #2 finished! INFO @ Tue, 14 Jul 2020 08:04:42: #2 predicted fragment length is 159 bps INFO @ Tue, 14 Jul 2020 08:04:42: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 14 Jul 2020 08:04:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.05_model.r INFO @ Tue, 14 Jul 2020 08:04:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:04:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:04:42: 10000000 INFO @ Tue, 14 Jul 2020 08:04:44: 15000000 INFO @ Tue, 14 Jul 2020 08:04:49: 11000000 INFO @ Tue, 14 Jul 2020 08:04:50: 16000000 INFO @ Tue, 14 Jul 2020 08:04:56: 12000000 INFO @ Tue, 14 Jul 2020 08:04:57: 17000000 INFO @ Tue, 14 Jul 2020 08:05:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:05:03: 13000000 INFO @ Tue, 14 Jul 2020 08:05:05: 18000000 INFO @ Tue, 14 Jul 2020 08:05:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:05:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:05:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:05:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.05_summits.bed INFO @ Tue, 14 Jul 2020 08:05:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5294 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:05:12: 19000000 INFO @ Tue, 14 Jul 2020 08:05:17: 15000000 INFO @ Tue, 14 Jul 2020 08:05:19: 20000000 INFO @ Tue, 14 Jul 2020 08:05:24: 16000000 INFO @ Tue, 14 Jul 2020 08:05:26: 21000000 INFO @ Tue, 14 Jul 2020 08:05:31: 17000000 INFO @ Tue, 14 Jul 2020 08:05:33: 22000000 INFO @ Tue, 14 Jul 2020 08:05:38: 18000000 INFO @ Tue, 14 Jul 2020 08:05:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:05:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:05:38: #1 total tags in treatment: 10514604 INFO @ Tue, 14 Jul 2020 08:05:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:05:38: #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 08:05:38: #1 tags after filtering in treatment: 9593563 INFO @ Tue, 14 Jul 2020 08:05:38: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:05:38: #1 finished! INFO @ Tue, 14 Jul 2020 08:05:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:05:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:05:39: #2 number of paired peaks: 357 WARNING @ Tue, 14 Jul 2020 08:05:39: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 14 Jul 2020 08:05:39: start model_add_line... INFO @ Tue, 14 Jul 2020 08:05:39: start X-correlation... INFO @ Tue, 14 Jul 2020 08:05:39: end of X-cor INFO @ Tue, 14 Jul 2020 08:05:39: #2 finished! INFO @ Tue, 14 Jul 2020 08:05:39: #2 predicted fragment length is 159 bps INFO @ Tue, 14 Jul 2020 08:05:39: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 14 Jul 2020 08:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.10_model.r INFO @ Tue, 14 Jul 2020 08:05:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:05:44: 19000000 INFO @ Tue, 14 Jul 2020 08:05:51: 20000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:05:57: 21000000 INFO @ Tue, 14 Jul 2020 08:05:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:06:04: 22000000 INFO @ Tue, 14 Jul 2020 08:06:09: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:06:09: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:06:09: #1 total tags in treatment: 10514604 INFO @ Tue, 14 Jul 2020 08:06:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:06:09: #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 08:06:09: #1 tags after filtering in treatment: 9593563 INFO @ Tue, 14 Jul 2020 08:06:09: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 08:06:09: #1 finished! INFO @ Tue, 14 Jul 2020 08:06:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.10_summits.bed INFO @ Tue, 14 Jul 2020 08:06:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2832 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:06:10: #2 number of paired peaks: 357 WARNING @ Tue, 14 Jul 2020 08:06:10: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 14 Jul 2020 08:06:10: start model_add_line... INFO @ Tue, 14 Jul 2020 08:06:10: start X-correlation... INFO @ Tue, 14 Jul 2020 08:06:10: end of X-cor INFO @ Tue, 14 Jul 2020 08:06:10: #2 finished! INFO @ Tue, 14 Jul 2020 08:06:10: #2 predicted fragment length is 159 bps INFO @ Tue, 14 Jul 2020 08:06:10: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 14 Jul 2020 08:06:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.20_model.r INFO @ Tue, 14 Jul 2020 08:06:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:06:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:06:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736496/SRX5736496.20_summits.bed INFO @ Tue, 14 Jul 2020 08:06:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1072 records, 4 fields): 12 millis CompletedMACS2peakCalling