Job ID = 8069717 SRX = SRX7917430 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:47:08 prefetch.2.10.7: 1) Downloading 'SRR11313011'... 2020-08-08T03:47:08 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:47:32 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:47:32 prefetch.2.10.7: 'SRR11313011' is valid 2020-08-08T03:47:32 prefetch.2.10.7: 1) 'SRR11313011' was downloaded successfully Read 1874950 spots for SRR11313011/SRR11313011.sra Written 1874950 spots for SRR11313011/SRR11313011.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070388 ("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: 00:02:19 1874950 reads; of these: 1874950 (100.00%) were paired; of these: 376243 (20.07%) aligned concordantly 0 times 1293496 (68.99%) aligned concordantly exactly 1 time 205211 (10.94%) aligned concordantly >1 times ---- 376243 pairs aligned concordantly 0 times; of these: 190049 (50.51%) aligned discordantly 1 time ---- 186194 pairs aligned 0 times concordantly or discordantly; of these: 372388 mates make up the pairs; of these: 212432 (57.05%) aligned 0 times 85261 (22.90%) aligned exactly 1 time 74695 (20.06%) aligned >1 times 94.33% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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] 727098 / 1682874 = 0.4321 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 @ Sat, 08 Aug 2020 12:51:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.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, 08 Aug 2020 12:51:14: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:14: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:51:20: 1000000 INFO @ Sat, 08 Aug 2020 12:51:25: 2000000 INFO @ Sat, 08 Aug 2020 12:51:26: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:51:26: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:51:26: #1 total tags in treatment: 817538 INFO @ Sat, 08 Aug 2020 12:51:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:51:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:51:26: #1 tags after filtering in treatment: 602033 INFO @ Sat, 08 Aug 2020 12:51:26: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 12:51:26: #1 finished! INFO @ Sat, 08 Aug 2020 12:51:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:51:26: #2 number of paired peaks: 4396 INFO @ Sat, 08 Aug 2020 12:51:26: start model_add_line... INFO @ Sat, 08 Aug 2020 12:51:26: start X-correlation... INFO @ Sat, 08 Aug 2020 12:51:26: end of X-cor INFO @ Sat, 08 Aug 2020 12:51:26: #2 finished! INFO @ Sat, 08 Aug 2020 12:51:26: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:51:26: #2 alternative fragment length(s) may be 3,188,203,226 bps INFO @ Sat, 08 Aug 2020 12:51:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.05_model.r INFO @ Sat, 08 Aug 2020 12:51:26: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:51:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:51:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:51:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:51:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:51:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.05_summits.bed INFO @ Sat, 08 Aug 2020 12:51:28: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (30 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 08 Aug 2020 12:51:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.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, 08 Aug 2020 12:51:44: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:51:44: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:51:50: 1000000 INFO @ Sat, 08 Aug 2020 12:51:55: 2000000 INFO @ Sat, 08 Aug 2020 12:51:56: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:51:56: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:51:56: #1 total tags in treatment: 817538 INFO @ Sat, 08 Aug 2020 12:51:56: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:51:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:51:56: #1 tags after filtering in treatment: 602033 INFO @ Sat, 08 Aug 2020 12:51:56: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 12:51:56: #1 finished! INFO @ Sat, 08 Aug 2020 12:51:56: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:51:56: #2 number of paired peaks: 4396 INFO @ Sat, 08 Aug 2020 12:51:56: start model_add_line... INFO @ Sat, 08 Aug 2020 12:51:56: start X-correlation... INFO @ Sat, 08 Aug 2020 12:51:56: end of X-cor INFO @ Sat, 08 Aug 2020 12:51:56: #2 finished! INFO @ Sat, 08 Aug 2020 12:51:56: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:51:56: #2 alternative fragment length(s) may be 3,188,203,226 bps INFO @ Sat, 08 Aug 2020 12:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.10_model.r INFO @ Sat, 08 Aug 2020 12:51:56: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:51:57: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:51:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:51:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:51:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.10_summits.bed INFO @ Sat, 08 Aug 2020 12:51:58: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Sat, 08 Aug 2020 12:52:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.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, 08 Aug 2020 12:52:14: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:52:14: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:52:20: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:52:25: 2000000 INFO @ Sat, 08 Aug 2020 12:52:26: #1 tag size is determined as 62 bps INFO @ Sat, 08 Aug 2020 12:52:26: #1 tag size = 62 INFO @ Sat, 08 Aug 2020 12:52:26: #1 total tags in treatment: 817538 INFO @ Sat, 08 Aug 2020 12:52:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:52:26: #1 tags after filtering in treatment: 602033 INFO @ Sat, 08 Aug 2020 12:52:26: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 08 Aug 2020 12:52:26: #1 finished! INFO @ Sat, 08 Aug 2020 12:52:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:52:26: #2 number of paired peaks: 4396 INFO @ Sat, 08 Aug 2020 12:52:26: start model_add_line... INFO @ Sat, 08 Aug 2020 12:52:26: start X-correlation... INFO @ Sat, 08 Aug 2020 12:52:26: end of X-cor INFO @ Sat, 08 Aug 2020 12:52:26: #2 finished! INFO @ Sat, 08 Aug 2020 12:52:26: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:52:26: #2 alternative fragment length(s) may be 3,188,203,226 bps INFO @ Sat, 08 Aug 2020 12:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.20_model.r INFO @ Sat, 08 Aug 2020 12:52:26: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:52:27: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7917430/SRX7917430.20_summits.bed INFO @ Sat, 08 Aug 2020 12:52:28: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling