Job ID = 14172316 SRX = SRX9281766 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2369407 spots for SRR12813273/SRR12813273.sra Written 2369407 spots for SRR12813273/SRR12813273.sra Read 2358075 spots for SRR12813274/SRR12813274.sra Written 2358075 spots for SRR12813274/SRR12813274.sra Read 2407986 spots for SRR12813275/SRR12813275.sra Written 2407986 spots for SRR12813275/SRR12813275.sra Read 2396519 spots for SRR12813276/SRR12813276.sra Written 2396519 spots for SRR12813276/SRR12813276.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172765 ("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: 00:01:18 9531987 reads; of these: 9531987 (100.00%) were paired; of these: 9303638 (97.60%) aligned concordantly 0 times 165192 (1.73%) aligned concordantly exactly 1 time 63157 (0.66%) aligned concordantly >1 times ---- 9303638 pairs aligned concordantly 0 times; of these: 574 (0.01%) aligned discordantly 1 time ---- 9303064 pairs aligned 0 times concordantly or discordantly; of these: 18606128 mates make up the pairs; of these: 18551248 (99.71%) aligned 0 times 16127 (0.09%) aligned exactly 1 time 38753 (0.21%) aligned >1 times 2.69% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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_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] 4883 / 228742 = 0.0213 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 15:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.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 15:08:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:08:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:08:59: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:08:59: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:08:59: #1 total tags in treatment: 223471 INFO @ Sat, 11 Dec 2021 15:08:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:08:59: #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 15:08:59: #1 tags after filtering in treatment: 221025 INFO @ Sat, 11 Dec 2021 15:08:59: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:08:59: #1 finished! INFO @ Sat, 11 Dec 2021 15:08:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:08:59: #2 number of paired peaks: 871 WARNING @ Sat, 11 Dec 2021 15:08:59: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Sat, 11 Dec 2021 15:08:59: start model_add_line... INFO @ Sat, 11 Dec 2021 15:08:59: start X-correlation... INFO @ Sat, 11 Dec 2021 15:08:59: end of X-cor INFO @ Sat, 11 Dec 2021 15:08:59: #2 finished! INFO @ Sat, 11 Dec 2021 15:08:59: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 15:08:59: #2 alternative fragment length(s) may be 102,204 bps INFO @ Sat, 11 Dec 2021 15:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.05_model.r INFO @ Sat, 11 Dec 2021 15:08:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:08:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:09:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:09:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:09:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.05_summits.bed INFO @ Sat, 11 Dec 2021 15:09:00: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 15:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.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 15:09:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:09:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:09:30: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:09:30: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:09:30: #1 total tags in treatment: 223471 INFO @ Sat, 11 Dec 2021 15:09:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:09:30: #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 15:09:30: #1 tags after filtering in treatment: 221025 INFO @ Sat, 11 Dec 2021 15:09:30: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:09:30: #1 finished! INFO @ Sat, 11 Dec 2021 15:09:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:09:30: #2 number of paired peaks: 871 WARNING @ Sat, 11 Dec 2021 15:09:30: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Sat, 11 Dec 2021 15:09:30: start model_add_line... INFO @ Sat, 11 Dec 2021 15:09:30: start X-correlation... INFO @ Sat, 11 Dec 2021 15:09:30: end of X-cor INFO @ Sat, 11 Dec 2021 15:09:30: #2 finished! INFO @ Sat, 11 Dec 2021 15:09:30: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 15:09:30: #2 alternative fragment length(s) may be 102,204 bps INFO @ Sat, 11 Dec 2021 15:09:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.10_model.r INFO @ Sat, 11 Dec 2021 15:09:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:09:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:09:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.10_summits.bed INFO @ Sat, 11 Dec 2021 15:09:30: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.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 15:09:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:09:58: #1 read treatment tags... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:10:01: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 15:10:01: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 15:10:01: #1 total tags in treatment: 223471 INFO @ Sat, 11 Dec 2021 15:10:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:10:01: #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 15:10:01: #1 tags after filtering in treatment: 221025 INFO @ Sat, 11 Dec 2021 15:10:01: #1 Redundant rate of treatment: 0.01 INFO @ Sat, 11 Dec 2021 15:10:01: #1 finished! INFO @ Sat, 11 Dec 2021 15:10:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:10:01: #2 number of paired peaks: 871 WARNING @ Sat, 11 Dec 2021 15:10:01: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Sat, 11 Dec 2021 15:10:01: start model_add_line... INFO @ Sat, 11 Dec 2021 15:10:01: start X-correlation... INFO @ Sat, 11 Dec 2021 15:10:01: end of X-cor INFO @ Sat, 11 Dec 2021 15:10:01: #2 finished! INFO @ Sat, 11 Dec 2021 15:10:01: #2 predicted fragment length is 102 bps INFO @ Sat, 11 Dec 2021 15:10:01: #2 alternative fragment length(s) may be 102,204 bps INFO @ Sat, 11 Dec 2021 15:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.20_model.r INFO @ Sat, 11 Dec 2021 15:10:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:10:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9281766/SRX9281766.20_summits.bed INFO @ Sat, 11 Dec 2021 15:10:02: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 13 millis CompletedMACS2peakCalling