Job ID = 5791026 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:19:36 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 ) 2020-04-21T23:19:36 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 ) 2020-04-21T23:19:36 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 : 3,135,003 reads read : 6,270,006 reads written : 6,270,006 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: 00:01:28 3135003 reads; of these: 3135003 (100.00%) were paired; of these: 2019745 (64.43%) aligned concordantly 0 times 891854 (28.45%) aligned concordantly exactly 1 time 223404 (7.13%) aligned concordantly >1 times ---- 2019745 pairs aligned concordantly 0 times; of these: 499 (0.02%) aligned discordantly 1 time ---- 2019246 pairs aligned 0 times concordantly or discordantly; of these: 4038492 mates make up the pairs; of these: 2127680 (52.69%) aligned 0 times 1493255 (36.98%) aligned exactly 1 time 417557 (10.34%) aligned >1 times 66.07% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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] 9142 / 1111766 = 0.0082 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 08:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.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 08:24:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:24:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:24:14: 1000000 INFO @ Wed, 22 Apr 2020 08:24:20: 2000000 INFO @ Wed, 22 Apr 2020 08:24:27: 3000000 INFO @ Wed, 22 Apr 2020 08:24:33: 4000000 INFO @ Wed, 22 Apr 2020 08:24:34: #1 tag size is determined as 70 bps INFO @ Wed, 22 Apr 2020 08:24:34: #1 tag size = 70 INFO @ Wed, 22 Apr 2020 08:24:34: #1 total tags in treatment: 1106117 INFO @ Wed, 22 Apr 2020 08:24:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:24:34: #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 08:24:34: #1 tags after filtering in treatment: 1004895 INFO @ Wed, 22 Apr 2020 08:24:34: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 22 Apr 2020 08:24:34: #1 finished! INFO @ Wed, 22 Apr 2020 08:24:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:24:34: #2 number of paired peaks: 156 WARNING @ Wed, 22 Apr 2020 08:24:34: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Wed, 22 Apr 2020 08:24:34: start model_add_line... INFO @ Wed, 22 Apr 2020 08:24:34: start X-correlation... INFO @ Wed, 22 Apr 2020 08:24:34: end of X-cor INFO @ Wed, 22 Apr 2020 08:24:34: #2 finished! INFO @ Wed, 22 Apr 2020 08:24:34: #2 predicted fragment length is 157 bps INFO @ Wed, 22 Apr 2020 08:24:34: #2 alternative fragment length(s) may be 3,157,192,598 bps INFO @ Wed, 22 Apr 2020 08:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.05_model.r INFO @ Wed, 22 Apr 2020 08:24:34: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:24:34: #3 Pre-compute pvalue-qvalue table... 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 08:24:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.05_summits.bed INFO @ Wed, 22 Apr 2020 08:24:38: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (289 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:24:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.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 08:24:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:24:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:24:44: 1000000 INFO @ Wed, 22 Apr 2020 08:24:50: 2000000 INFO @ Wed, 22 Apr 2020 08:24:56: 3000000 INFO @ Wed, 22 Apr 2020 08:25:02: 4000000 INFO @ Wed, 22 Apr 2020 08:25:03: #1 tag size is determined as 70 bps INFO @ Wed, 22 Apr 2020 08:25:03: #1 tag size = 70 INFO @ Wed, 22 Apr 2020 08:25:03: #1 total tags in treatment: 1106117 INFO @ Wed, 22 Apr 2020 08:25:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:25:03: #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 08:25:03: #1 tags after filtering in treatment: 1004895 INFO @ Wed, 22 Apr 2020 08:25:03: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 22 Apr 2020 08:25:03: #1 finished! INFO @ Wed, 22 Apr 2020 08:25:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:25:03: #2 number of paired peaks: 156 WARNING @ Wed, 22 Apr 2020 08:25:03: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Wed, 22 Apr 2020 08:25:03: start model_add_line... INFO @ Wed, 22 Apr 2020 08:25:03: start X-correlation... INFO @ Wed, 22 Apr 2020 08:25:03: end of X-cor INFO @ Wed, 22 Apr 2020 08:25:03: #2 finished! INFO @ Wed, 22 Apr 2020 08:25:03: #2 predicted fragment length is 157 bps INFO @ Wed, 22 Apr 2020 08:25:03: #2 alternative fragment length(s) may be 3,157,192,598 bps INFO @ Wed, 22 Apr 2020 08:25:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.10_model.r INFO @ Wed, 22 Apr 2020 08:25:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:25:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:25:06: #3 Call peaks for each chromosome... 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 08:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.10_summits.bed INFO @ Wed, 22 Apr 2020 08:25:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (158 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.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 08:25:08: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:25:08: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:25:14: 1000000 INFO @ Wed, 22 Apr 2020 08:25:20: 2000000 INFO @ Wed, 22 Apr 2020 08:25:26: 3000000 INFO @ Wed, 22 Apr 2020 08:25:32: 4000000 INFO @ Wed, 22 Apr 2020 08:25:33: #1 tag size is determined as 70 bps INFO @ Wed, 22 Apr 2020 08:25:33: #1 tag size = 70 INFO @ Wed, 22 Apr 2020 08:25:33: #1 total tags in treatment: 1106117 INFO @ Wed, 22 Apr 2020 08:25:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:25:33: #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 08:25:33: #1 tags after filtering in treatment: 1004895 INFO @ Wed, 22 Apr 2020 08:25:33: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 22 Apr 2020 08:25:33: #1 finished! INFO @ Wed, 22 Apr 2020 08:25:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:25:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:25:33: #2 number of paired peaks: 156 WARNING @ Wed, 22 Apr 2020 08:25:33: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Wed, 22 Apr 2020 08:25:33: start model_add_line... INFO @ Wed, 22 Apr 2020 08:25:33: start X-correlation... INFO @ Wed, 22 Apr 2020 08:25:33: end of X-cor INFO @ Wed, 22 Apr 2020 08:25:33: #2 finished! INFO @ Wed, 22 Apr 2020 08:25:33: #2 predicted fragment length is 157 bps INFO @ Wed, 22 Apr 2020 08:25:33: #2 alternative fragment length(s) may be 3,157,192,598 bps INFO @ Wed, 22 Apr 2020 08:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.20_model.r INFO @ Wed, 22 Apr 2020 08:25:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:25:36: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:25:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:25:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:25:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874522/SRX5874522.20_summits.bed INFO @ Wed, 22 Apr 2020 08:25:37: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (70 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。