Job ID = 6626489 SRX = SRX5736469 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7194677 spots for SRR8956881/SRR8956881.sra Written 7194677 spots for SRR8956881/SRR8956881.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626652 ("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: 00:16:41 7194677 reads; of these: 7194677 (100.00%) were paired; of these: 1343834 (18.68%) aligned concordantly 0 times 4588529 (63.78%) aligned concordantly exactly 1 time 1262314 (17.55%) aligned concordantly >1 times ---- 1343834 pairs aligned concordantly 0 times; of these: 101314 (7.54%) aligned discordantly 1 time ---- 1242520 pairs aligned 0 times concordantly or discordantly; of these: 2485040 mates make up the pairs; of these: 2039186 (82.06%) aligned 0 times 162438 (6.54%) aligned exactly 1 time 283416 (11.40%) aligned >1 times 85.83% overall alignment rate Time searching: 00:16:41 Overall time: 00:16:41 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] 469252 / 5940416 = 0.0790 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 07:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.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 07:28:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:01: 1000000 INFO @ Tue, 14 Jul 2020 07:29:07: 2000000 INFO @ Tue, 14 Jul 2020 07:29:14: 3000000 INFO @ Tue, 14 Jul 2020 07:29:21: 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 07:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.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 07:29:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:28: 5000000 INFO @ Tue, 14 Jul 2020 07:29:32: 1000000 INFO @ Tue, 14 Jul 2020 07:29:36: 6000000 INFO @ Tue, 14 Jul 2020 07:29:40: 2000000 INFO @ Tue, 14 Jul 2020 07:29:45: 7000000 INFO @ Tue, 14 Jul 2020 07:29:49: 3000000 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 07:29:53: 8000000 INFO @ Tue, 14 Jul 2020 07:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.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 07:29:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:57: 4000000 INFO @ Tue, 14 Jul 2020 07:30:02: 9000000 INFO @ Tue, 14 Jul 2020 07:30:04: 1000000 INFO @ Tue, 14 Jul 2020 07:30:06: 5000000 INFO @ Tue, 14 Jul 2020 07:30:12: 10000000 INFO @ Tue, 14 Jul 2020 07:30:13: 2000000 INFO @ Tue, 14 Jul 2020 07:30:15: 6000000 INFO @ Tue, 14 Jul 2020 07:30:21: 11000000 INFO @ Tue, 14 Jul 2020 07:30:22: 3000000 INFO @ Tue, 14 Jul 2020 07:30:24: 7000000 INFO @ Tue, 14 Jul 2020 07:30:24: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:30:24: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:30:24: #1 total tags in treatment: 5385139 INFO @ Tue, 14 Jul 2020 07:30:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:24: #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 07:30:25: #1 tags after filtering in treatment: 5028310 INFO @ Tue, 14 Jul 2020 07:30:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:30:25: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:25: #2 number of paired peaks: 525 WARNING @ Tue, 14 Jul 2020 07:30:25: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 14 Jul 2020 07:30:25: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:25: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:25: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:25: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:25: #2 predicted fragment length is 228 bps INFO @ Tue, 14 Jul 2020 07:30:25: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 14 Jul 2020 07:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.05_model.r INFO @ Tue, 14 Jul 2020 07:30:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:30:32: 4000000 INFO @ Tue, 14 Jul 2020 07:30:32: 8000000 INFO @ Tue, 14 Jul 2020 07:30:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:41: 5000000 INFO @ Tue, 14 Jul 2020 07:30:41: 9000000 INFO @ Tue, 14 Jul 2020 07:30:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.05_summits.bed INFO @ Tue, 14 Jul 2020 07:30:42: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3928 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:30:49: 6000000 INFO @ Tue, 14 Jul 2020 07:30:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:30:58: 7000000 INFO @ Tue, 14 Jul 2020 07:30:59: 11000000 INFO @ Tue, 14 Jul 2020 07:31:03: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:31:03: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:31:03: #1 total tags in treatment: 5385139 INFO @ Tue, 14 Jul 2020 07:31:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:31:03: #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 07:31:03: #1 tags after filtering in treatment: 5028310 INFO @ Tue, 14 Jul 2020 07:31:03: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:31:03: #1 finished! INFO @ Tue, 14 Jul 2020 07:31:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:31:03: #2 number of paired peaks: 525 WARNING @ Tue, 14 Jul 2020 07:31:03: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 14 Jul 2020 07:31:03: start model_add_line... INFO @ Tue, 14 Jul 2020 07:31:03: start X-correlation... INFO @ Tue, 14 Jul 2020 07:31:03: end of X-cor INFO @ Tue, 14 Jul 2020 07:31:03: #2 finished! INFO @ Tue, 14 Jul 2020 07:31:03: #2 predicted fragment length is 228 bps INFO @ Tue, 14 Jul 2020 07:31:03: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 14 Jul 2020 07:31:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.10_model.r INFO @ Tue, 14 Jul 2020 07:31:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:31:07: 8000000 INFO @ Tue, 14 Jul 2020 07:31:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:31:16: 9000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:31:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:31:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:31:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.10_summits.bed INFO @ Tue, 14 Jul 2020 07:31:20: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1920 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:31:24: 10000000 INFO @ Tue, 14 Jul 2020 07:31:32: 11000000 INFO @ Tue, 14 Jul 2020 07:31:36: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:31:36: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:31:36: #1 total tags in treatment: 5385139 INFO @ Tue, 14 Jul 2020 07:31:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:31:36: #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 07:31:36: #1 tags after filtering in treatment: 5028310 INFO @ Tue, 14 Jul 2020 07:31:36: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 14 Jul 2020 07:31:36: #1 finished! INFO @ Tue, 14 Jul 2020 07:31:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:31:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:31:36: #2 number of paired peaks: 525 WARNING @ Tue, 14 Jul 2020 07:31:36: Fewer paired peaks (525) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 525 pairs to build model! INFO @ Tue, 14 Jul 2020 07:31:36: start model_add_line... INFO @ Tue, 14 Jul 2020 07:31:36: start X-correlation... INFO @ Tue, 14 Jul 2020 07:31:36: end of X-cor INFO @ Tue, 14 Jul 2020 07:31:36: #2 finished! INFO @ Tue, 14 Jul 2020 07:31:36: #2 predicted fragment length is 228 bps INFO @ Tue, 14 Jul 2020 07:31:36: #2 alternative fragment length(s) may be 228 bps INFO @ Tue, 14 Jul 2020 07:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.20_model.r INFO @ Tue, 14 Jul 2020 07:31:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:31:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:31:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:31:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:31:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736469/SRX5736469.20_summits.bed INFO @ Tue, 14 Jul 2020 07:31:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 1 millis CompletedMACS2peakCalling