Job ID = 5791267 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:16:10 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 4,943,602 reads read : 9,887,204 reads written : 9,887,204 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:54 4943602 reads; of these: 4943602 (100.00%) were paired; of these: 417256 (8.44%) aligned concordantly 0 times 4021149 (81.34%) aligned concordantly exactly 1 time 505197 (10.22%) aligned concordantly >1 times ---- 417256 pairs aligned concordantly 0 times; of these: 51294 (12.29%) aligned discordantly 1 time ---- 365962 pairs aligned 0 times concordantly or discordantly; of these: 731924 mates make up the pairs; of these: 650381 (88.86%) aligned 0 times 59350 (8.11%) aligned exactly 1 time 22193 (3.03%) aligned >1 times 93.42% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 1905158 / 4531639 = 0.4204 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 @ Wed, 22 Apr 2020 09:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:22:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:22:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:22:09: 1000000 INFO @ Wed, 22 Apr 2020 09:22:13: 2000000 INFO @ Wed, 22 Apr 2020 09:22:17: 3000000 INFO @ Wed, 22 Apr 2020 09:22:21: 4000000 INFO @ Wed, 22 Apr 2020 09:22:25: 5000000 INFO @ Wed, 22 Apr 2020 09:22:27: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:22:27: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:22:27: #1 total tags in treatment: 2622206 INFO @ Wed, 22 Apr 2020 09:22:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:22:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:22:27: #1 tags after filtering in treatment: 1367676 INFO @ Wed, 22 Apr 2020 09:22:27: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 09:22:27: #1 finished! INFO @ Wed, 22 Apr 2020 09:22:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:22:27: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 09:22:27: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 09:22:27: start model_add_line... INFO @ Wed, 22 Apr 2020 09:22:27: start X-correlation... INFO @ Wed, 22 Apr 2020 09:22:27: end of X-cor INFO @ Wed, 22 Apr 2020 09:22:27: #2 finished! INFO @ Wed, 22 Apr 2020 09:22:27: #2 predicted fragment length is 63 bps INFO @ Wed, 22 Apr 2020 09:22:27: #2 alternative fragment length(s) may be 2,63 bps INFO @ Wed, 22 Apr 2020 09:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.05_model.r INFO @ Wed, 22 Apr 2020 09:22:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:22:30: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:22:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:22:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:22:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.05_summits.bed INFO @ Wed, 22 Apr 2020 09:22:31: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (3883 records, 4 fields): 5 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 @ Wed, 22 Apr 2020 09:22:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:22:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:22:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:22:39: 1000000 INFO @ Wed, 22 Apr 2020 09:22:43: 2000000 INFO @ Wed, 22 Apr 2020 09:22:47: 3000000 INFO @ Wed, 22 Apr 2020 09:22:51: 4000000 INFO @ Wed, 22 Apr 2020 09:22:55: 5000000 INFO @ Wed, 22 Apr 2020 09:22:57: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:22:57: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:22:57: #1 total tags in treatment: 2622206 INFO @ Wed, 22 Apr 2020 09:22:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:22:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:22:57: #1 tags after filtering in treatment: 1367676 INFO @ Wed, 22 Apr 2020 09:22:57: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 09:22:57: #1 finished! INFO @ Wed, 22 Apr 2020 09:22:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:22:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:22:57: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 09:22:57: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 09:22:57: start model_add_line... INFO @ Wed, 22 Apr 2020 09:22:57: start X-correlation... INFO @ Wed, 22 Apr 2020 09:22:57: end of X-cor INFO @ Wed, 22 Apr 2020 09:22:57: #2 finished! INFO @ Wed, 22 Apr 2020 09:22:57: #2 predicted fragment length is 63 bps INFO @ Wed, 22 Apr 2020 09:22:57: #2 alternative fragment length(s) may be 2,63 bps INFO @ Wed, 22 Apr 2020 09:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.10_model.r INFO @ Wed, 22 Apr 2020 09:22:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:23:00: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:23:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:23:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.10_summits.bed INFO @ Wed, 22 Apr 2020 09:23:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (2255 records, 4 fields): 9 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 @ Wed, 22 Apr 2020 09:23:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 09:23:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:23:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:23:09: 1000000 INFO @ Wed, 22 Apr 2020 09:23:13: 2000000 INFO @ Wed, 22 Apr 2020 09:23:17: 3000000 INFO @ Wed, 22 Apr 2020 09:23:21: 4000000 INFO @ Wed, 22 Apr 2020 09:23:25: 5000000 INFO @ Wed, 22 Apr 2020 09:23:27: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:23:27: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:23:27: #1 total tags in treatment: 2622206 INFO @ Wed, 22 Apr 2020 09:23:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:23:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:23:27: #1 tags after filtering in treatment: 1367676 INFO @ Wed, 22 Apr 2020 09:23:27: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 09:23:27: #1 finished! INFO @ Wed, 22 Apr 2020 09:23:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:23:27: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 09:23:27: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 09:23:27: start model_add_line... INFO @ Wed, 22 Apr 2020 09:23:27: start X-correlation... INFO @ Wed, 22 Apr 2020 09:23:27: end of X-cor INFO @ Wed, 22 Apr 2020 09:23:27: #2 finished! INFO @ Wed, 22 Apr 2020 09:23:27: #2 predicted fragment length is 63 bps INFO @ Wed, 22 Apr 2020 09:23:27: #2 alternative fragment length(s) may be 2,63 bps INFO @ Wed, 22 Apr 2020 09:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.20_model.r INFO @ Wed, 22 Apr 2020 09:23:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:23:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:23:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:23:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:23:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388408/SRX7388408.20_summits.bed INFO @ Wed, 22 Apr 2020 09:23:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。