Job ID = 5790815 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T22:40:59 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 ) 2020-04-21T22:46:43 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 : 12,805,210 reads read : 25,610,420 reads written : 25,610,420 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: 00:06:00 12805210 reads; of these: 12805210 (100.00%) were paired; of these: 6072231 (47.42%) aligned concordantly 0 times 5551977 (43.36%) aligned concordantly exactly 1 time 1181002 (9.22%) aligned concordantly >1 times ---- 6072231 pairs aligned concordantly 0 times; of these: 22992 (0.38%) aligned discordantly 1 time ---- 6049239 pairs aligned 0 times concordantly or discordantly; of these: 12098478 mates make up the pairs; of these: 12055044 (99.64%) aligned 0 times 24919 (0.21%) aligned exactly 1 time 18515 (0.15%) aligned >1 times 52.93% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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_sort_core] merging from 8 files... [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] 3638011 / 6752512 = 0.5388 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 08:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.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 08:12:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:06: 1000000 INFO @ Wed, 22 Apr 2020 08:12:12: 2000000 INFO @ Wed, 22 Apr 2020 08:12:17: 3000000 INFO @ Wed, 22 Apr 2020 08:12:22: 4000000 INFO @ Wed, 22 Apr 2020 08:12:27: 5000000 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 08:12:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.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 08:12:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:12:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:12:33: 6000000 INFO @ Wed, 22 Apr 2020 08:12:34: #1 tag size is determined as 100 bps INFO @ Wed, 22 Apr 2020 08:12:34: #1 tag size = 100 INFO @ Wed, 22 Apr 2020 08:12:34: #1 total tags in treatment: 3102596 INFO @ Wed, 22 Apr 2020 08:12:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:12:34: #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 08:12:34: #1 tags after filtering in treatment: 2014420 INFO @ Wed, 22 Apr 2020 08:12:34: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 08:12:34: #1 finished! INFO @ Wed, 22 Apr 2020 08:12:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:12:34: #2 number of paired peaks: 154 WARNING @ Wed, 22 Apr 2020 08:12:34: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 22 Apr 2020 08:12:34: start model_add_line... INFO @ Wed, 22 Apr 2020 08:12:34: start X-correlation... INFO @ Wed, 22 Apr 2020 08:12:34: end of X-cor INFO @ Wed, 22 Apr 2020 08:12:34: #2 finished! INFO @ Wed, 22 Apr 2020 08:12:34: #2 predicted fragment length is 183 bps INFO @ Wed, 22 Apr 2020 08:12:34: #2 alternative fragment length(s) may be 183 bps INFO @ Wed, 22 Apr 2020 08:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.05_model.r WARNING @ Wed, 22 Apr 2020 08:12:34: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:12:34: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Wed, 22 Apr 2020 08:12:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:12:34: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:12:36: 1000000 INFO @ Wed, 22 Apr 2020 08:12:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:12:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:12:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:12:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.05_summits.bed INFO @ Wed, 22 Apr 2020 08:12:41: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (503 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:12:42: 2000000 INFO @ Wed, 22 Apr 2020 08:12:47: 3000000 INFO @ Wed, 22 Apr 2020 08:12:52: 4000000 INFO @ Wed, 22 Apr 2020 08:12:58: 5000000 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 08:13:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.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 08:13:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:03: 6000000 INFO @ Wed, 22 Apr 2020 08:13:05: #1 tag size is determined as 100 bps INFO @ Wed, 22 Apr 2020 08:13:05: #1 tag size = 100 INFO @ Wed, 22 Apr 2020 08:13:05: #1 total tags in treatment: 3102596 INFO @ Wed, 22 Apr 2020 08:13:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:05: #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 08:13:05: #1 tags after filtering in treatment: 2014420 INFO @ Wed, 22 Apr 2020 08:13:05: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 08:13:05: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:05: #2 number of paired peaks: 154 WARNING @ Wed, 22 Apr 2020 08:13:05: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:05: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:05: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:05: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:05: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:05: #2 predicted fragment length is 183 bps INFO @ Wed, 22 Apr 2020 08:13:05: #2 alternative fragment length(s) may be 183 bps INFO @ Wed, 22 Apr 2020 08:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.10_model.r WARNING @ Wed, 22 Apr 2020 08:13:05: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:05: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Wed, 22 Apr 2020 08:13:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:13:05: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:06: 1000000 INFO @ Wed, 22 Apr 2020 08:13:09: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.10_summits.bed INFO @ Wed, 22 Apr 2020 08:13:11: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (288 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:13:12: 2000000 INFO @ Wed, 22 Apr 2020 08:13:17: 3000000 INFO @ Wed, 22 Apr 2020 08:13:23: 4000000 INFO @ Wed, 22 Apr 2020 08:13:28: 5000000 INFO @ Wed, 22 Apr 2020 08:13:34: 6000000 INFO @ Wed, 22 Apr 2020 08:13:35: #1 tag size is determined as 100 bps INFO @ Wed, 22 Apr 2020 08:13:35: #1 tag size = 100 INFO @ Wed, 22 Apr 2020 08:13:35: #1 total tags in treatment: 3102596 INFO @ Wed, 22 Apr 2020 08:13:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:35: #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 08:13:35: #1 tags after filtering in treatment: 2014420 INFO @ Wed, 22 Apr 2020 08:13:35: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 08:13:35: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:35: #2 number of paired peaks: 154 WARNING @ Wed, 22 Apr 2020 08:13:35: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:35: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:35: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:35: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:35: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:35: #2 predicted fragment length is 183 bps INFO @ Wed, 22 Apr 2020 08:13:35: #2 alternative fragment length(s) may be 183 bps INFO @ Wed, 22 Apr 2020 08:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.20_model.r WARNING @ Wed, 22 Apr 2020 08:13:35: #2 Since the d (183) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:35: #2 You may need to consider one of the other alternative d(s): 183 WARNING @ Wed, 22 Apr 2020 08:13:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:13:35: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/DRX137664/DRX137664.20_summits.bed INFO @ Wed, 22 Apr 2020 08:13:42: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。