Job ID = 5791279 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:22:34 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 : 17,194,725 reads read : 34,389,450 reads written : 34,389,450 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: 00:02:33 17194725 reads; of these: 17194725 (100.00%) were paired; of these: 16627643 (96.70%) aligned concordantly 0 times 469816 (2.73%) aligned concordantly exactly 1 time 97266 (0.57%) aligned concordantly >1 times ---- 16627643 pairs aligned concordantly 0 times; of these: 548723 (3.30%) aligned discordantly 1 time ---- 16078920 pairs aligned 0 times concordantly or discordantly; of these: 32157840 mates make up the pairs; of these: 30176689 (93.84%) aligned 0 times 1513200 (4.71%) aligned exactly 1 time 467951 (1.46%) aligned >1 times 12.25% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 917411 / 1089601 = 0.8420 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 09:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.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 09:32:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:32:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:32:12: 1000000 INFO @ Wed, 22 Apr 2020 09:32:19: 2000000 INFO @ Wed, 22 Apr 2020 09:32:21: #1 tag size is determined as 55 bps INFO @ Wed, 22 Apr 2020 09:32:21: #1 tag size = 55 INFO @ Wed, 22 Apr 2020 09:32:21: #1 total tags in treatment: 112071 INFO @ Wed, 22 Apr 2020 09:32:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:32:21: #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 09:32:21: #1 tags after filtering in treatment: 98878 INFO @ Wed, 22 Apr 2020 09:32:21: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 09:32:21: #1 finished! INFO @ Wed, 22 Apr 2020 09:32:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:32:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:32:21: #2 number of paired peaks: 42 WARNING @ Wed, 22 Apr 2020 09:32:21: Too few paired peaks (42) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 09:32:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.05_peaks.narrowPeak’: No such file or directory 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 09:32:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.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 09:32:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:32:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:32:38: 1000000 INFO @ Wed, 22 Apr 2020 09:32:43: 2000000 INFO @ Wed, 22 Apr 2020 09:32:44: #1 tag size is determined as 55 bps INFO @ Wed, 22 Apr 2020 09:32:44: #1 tag size = 55 INFO @ Wed, 22 Apr 2020 09:32:44: #1 total tags in treatment: 112071 INFO @ Wed, 22 Apr 2020 09:32:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:32:44: #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 09:32:44: #1 tags after filtering in treatment: 98878 INFO @ Wed, 22 Apr 2020 09:32:44: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 09:32:44: #1 finished! INFO @ Wed, 22 Apr 2020 09:32:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:32:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:32:44: #2 number of paired peaks: 42 WARNING @ Wed, 22 Apr 2020 09:32:44: Too few paired peaks (42) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 09:32:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.10_peaks.narrowPeak’: No such file or directory 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 09:33:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.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 09:33:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:33:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:33:10: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:33:16: 2000000 INFO @ Wed, 22 Apr 2020 09:33:18: #1 tag size is determined as 55 bps INFO @ Wed, 22 Apr 2020 09:33:18: #1 tag size = 55 INFO @ Wed, 22 Apr 2020 09:33:18: #1 total tags in treatment: 112071 INFO @ Wed, 22 Apr 2020 09:33:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:33:18: #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 09:33:18: #1 tags after filtering in treatment: 98878 INFO @ Wed, 22 Apr 2020 09:33:18: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Apr 2020 09:33:18: #1 finished! INFO @ Wed, 22 Apr 2020 09:33:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:33:18: #2 number of paired peaks: 42 WARNING @ Wed, 22 Apr 2020 09:33:18: Too few paired peaks (42) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Wed, 22 Apr 2020 09:33:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7399910/SRX7399910.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling