Job ID = 5791762 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:38:23 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 ) 2020-04-22T01:40:56 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 ) 2020-04-22T01:40:56 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 ) 2020-04-22T01:42:52 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 ) 2020-04-22T01:42:52 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 : 2,818,289 reads read : 5,636,578 reads written : 5,636,578 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: 00:02:07 2818289 reads; of these: 2818289 (100.00%) were paired; of these: 248367 (8.81%) aligned concordantly 0 times 2316720 (82.20%) aligned concordantly exactly 1 time 253202 (8.98%) aligned concordantly >1 times ---- 248367 pairs aligned concordantly 0 times; of these: 156405 (62.97%) aligned discordantly 1 time ---- 91962 pairs aligned 0 times concordantly or discordantly; of these: 183924 mates make up the pairs; of these: 117448 (63.86%) aligned 0 times 27664 (15.04%) aligned exactly 1 time 38812 (21.10%) aligned >1 times 97.92% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 63612 / 2722769 = 0.0234 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 10:48:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.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 10:48:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:48:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:48:13: 1000000 INFO @ Wed, 22 Apr 2020 10:48:19: 2000000 INFO @ Wed, 22 Apr 2020 10:48:25: 3000000 INFO @ Wed, 22 Apr 2020 10:48:31: 4000000 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 10:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.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 10:48:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:48:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:48:38: 5000000 INFO @ Wed, 22 Apr 2020 10:48:41: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:48:41: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:48:41: #1 total tags in treatment: 2508622 INFO @ Wed, 22 Apr 2020 10:48:41: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:48:41: #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 10:48:41: #1 tags after filtering in treatment: 2209346 INFO @ Wed, 22 Apr 2020 10:48:41: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 10:48:41: #1 finished! INFO @ Wed, 22 Apr 2020 10:48:41: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:48:41: #2 number of paired peaks: 182 WARNING @ Wed, 22 Apr 2020 10:48:41: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 22 Apr 2020 10:48:41: start model_add_line... INFO @ Wed, 22 Apr 2020 10:48:41: start X-correlation... INFO @ Wed, 22 Apr 2020 10:48:41: end of X-cor INFO @ Wed, 22 Apr 2020 10:48:41: #2 finished! INFO @ Wed, 22 Apr 2020 10:48:41: #2 predicted fragment length is 292 bps INFO @ Wed, 22 Apr 2020 10:48:41: #2 alternative fragment length(s) may be 1,193,198,265,270,292,298,352,402 bps INFO @ Wed, 22 Apr 2020 10:48:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.05_model.r INFO @ Wed, 22 Apr 2020 10:48:41: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:48:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:48:44: 1000000 INFO @ Wed, 22 Apr 2020 10:48:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:48:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.05_peaks.xls INFO @ Wed, 22 Apr 2020 10:48:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:48:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.05_summits.bed INFO @ Wed, 22 Apr 2020 10:48:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:48:51: 2000000 INFO @ Wed, 22 Apr 2020 10:48:59: 3000000 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 10:49:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.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 10:49:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:49:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:49:07: 4000000 INFO @ Wed, 22 Apr 2020 10:49:13: 1000000 INFO @ Wed, 22 Apr 2020 10:49:14: 5000000 INFO @ Wed, 22 Apr 2020 10:49:17: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:49:17: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:49:17: #1 total tags in treatment: 2508622 INFO @ Wed, 22 Apr 2020 10:49:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:49:17: #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 10:49:17: #1 tags after filtering in treatment: 2209346 INFO @ Wed, 22 Apr 2020 10:49:17: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 10:49:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:49:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:49:17: #2 number of paired peaks: 182 WARNING @ Wed, 22 Apr 2020 10:49:17: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 22 Apr 2020 10:49:17: start model_add_line... INFO @ Wed, 22 Apr 2020 10:49:17: start X-correlation... INFO @ Wed, 22 Apr 2020 10:49:17: end of X-cor INFO @ Wed, 22 Apr 2020 10:49:17: #2 finished! INFO @ Wed, 22 Apr 2020 10:49:17: #2 predicted fragment length is 292 bps INFO @ Wed, 22 Apr 2020 10:49:17: #2 alternative fragment length(s) may be 1,193,198,265,270,292,298,352,402 bps INFO @ Wed, 22 Apr 2020 10:49:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.10_model.r INFO @ Wed, 22 Apr 2020 10:49:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:49:21: 2000000 INFO @ Wed, 22 Apr 2020 10:49:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:49:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.10_peaks.xls INFO @ Wed, 22 Apr 2020 10:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.10_summits.bed INFO @ Wed, 22 Apr 2020 10:49:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (522 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:49:27: 3000000 INFO @ Wed, 22 Apr 2020 10:49:35: 4000000 INFO @ Wed, 22 Apr 2020 10:49:41: 5000000 INFO @ Wed, 22 Apr 2020 10:49:44: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:49:44: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:49:44: #1 total tags in treatment: 2508622 INFO @ Wed, 22 Apr 2020 10:49:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:49:44: #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 10:49:44: #1 tags after filtering in treatment: 2209346 INFO @ Wed, 22 Apr 2020 10:49:44: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 10:49:44: #1 finished! INFO @ Wed, 22 Apr 2020 10:49:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:49:44: #2 number of paired peaks: 182 WARNING @ Wed, 22 Apr 2020 10:49:44: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Wed, 22 Apr 2020 10:49:44: start model_add_line... INFO @ Wed, 22 Apr 2020 10:49:44: start X-correlation... INFO @ Wed, 22 Apr 2020 10:49:44: end of X-cor INFO @ Wed, 22 Apr 2020 10:49:44: #2 finished! INFO @ Wed, 22 Apr 2020 10:49:44: #2 predicted fragment length is 292 bps INFO @ Wed, 22 Apr 2020 10:49:44: #2 alternative fragment length(s) may be 1,193,198,265,270,292,298,352,402 bps INFO @ Wed, 22 Apr 2020 10:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.20_model.r INFO @ Wed, 22 Apr 2020 10:49:44: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:49:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:49:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.20_peaks.xls INFO @ Wed, 22 Apr 2020 10:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741027/SRX7741027.20_summits.bed INFO @ Wed, 22 Apr 2020 10:49:51: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (335 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。