Job ID = 5790974 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:09:52 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 : 2,955,931 reads read : 5,911,862 reads written : 5,911,862 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: 00:01:50 2955931 reads; of these: 2955931 (100.00%) were paired; of these: 156953 (5.31%) aligned concordantly 0 times 2545394 (86.11%) aligned concordantly exactly 1 time 253584 (8.58%) aligned concordantly >1 times ---- 156953 pairs aligned concordantly 0 times; of these: 1260 (0.80%) aligned discordantly 1 time ---- 155693 pairs aligned 0 times concordantly or discordantly; of these: 311386 mates make up the pairs; of these: 296345 (95.17%) aligned 0 times 12629 (4.06%) aligned exactly 1 time 2412 (0.77%) aligned >1 times 94.99% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 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] 21000 / 2779611 = 0.0076 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 08:15:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.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 08:15:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:27: 1000000 INFO @ Wed, 22 Apr 2020 08:15:33: 2000000 INFO @ Wed, 22 Apr 2020 08:15:39: 3000000 INFO @ Wed, 22 Apr 2020 08:15:45: 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 08:15:50: 5000000 INFO @ Wed, 22 Apr 2020 08:15:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.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 08:15:51: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:51: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:54: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:54: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:54: #1 total tags in treatment: 2777979 INFO @ Wed, 22 Apr 2020 08:15:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:54: #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 08:15:54: #1 tags after filtering in treatment: 2593790 INFO @ Wed, 22 Apr 2020 08:15:54: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 22 Apr 2020 08:15:54: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:54: #2 number of paired peaks: 25 WARNING @ Wed, 22 Apr 2020 08:15:54: Too few paired peaks (25) 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 08:15:54: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.05_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/SRX5874479/SRX5874479.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:15:57: 1000000 INFO @ Wed, 22 Apr 2020 08:16:02: 2000000 INFO @ Wed, 22 Apr 2020 08:16:08: 3000000 INFO @ Wed, 22 Apr 2020 08:16:13: 4000000 INFO @ Wed, 22 Apr 2020 08:16:19: 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 08:16:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.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 08:16:21: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:21: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:22: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:22: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:22: #1 total tags in treatment: 2777979 INFO @ Wed, 22 Apr 2020 08:16:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:22: #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 08:16:22: #1 tags after filtering in treatment: 2593790 INFO @ Wed, 22 Apr 2020 08:16:22: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 22 Apr 2020 08:16:22: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:22: #2 number of paired peaks: 25 WARNING @ Wed, 22 Apr 2020 08:16:22: Too few paired peaks (25) 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 08:16:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.10_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/SRX5874479/SRX5874479.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:28: 1000000 INFO @ Wed, 22 Apr 2020 08:16:34: 2000000 INFO @ Wed, 22 Apr 2020 08:16:41: 3000000 INFO @ Wed, 22 Apr 2020 08:16:47: 4000000 INFO @ Wed, 22 Apr 2020 08:16:54: 5000000 INFO @ Wed, 22 Apr 2020 08:16:58: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:58: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:58: #1 total tags in treatment: 2777979 INFO @ Wed, 22 Apr 2020 08:16:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:58: #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 08:16:58: #1 tags after filtering in treatment: 2593790 INFO @ Wed, 22 Apr 2020 08:16:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 22 Apr 2020 08:16:58: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:58: #2 number of paired peaks: 25 WARNING @ Wed, 22 Apr 2020 08:16:58: Too few paired peaks (25) 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 08:16:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.20_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/SRX5874479/SRX5874479.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874479/SRX5874479.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。