Job ID = 5791069 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:25:48 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 ) 2020-04-21T23:25:48 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 ) 2020-04-21T23:25:48 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 ) 2020-04-21T23:25:48 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 : 9,573,342 reads read : 19,146,684 reads written : 19,146,684 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: 00:03:12 9573342 reads; of these: 9573342 (100.00%) were paired; of these: 3395186 (35.47%) aligned concordantly 0 times 5693092 (59.47%) aligned concordantly exactly 1 time 485064 (5.07%) aligned concordantly >1 times ---- 3395186 pairs aligned concordantly 0 times; of these: 238280 (7.02%) aligned discordantly 1 time ---- 3156906 pairs aligned 0 times concordantly or discordantly; of these: 6313812 mates make up the pairs; of these: 4621745 (73.20%) aligned 0 times 1529871 (24.23%) aligned exactly 1 time 162196 (2.57%) aligned >1 times 75.86% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 276657 / 6372640 = 0.0434 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 08:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.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 08:38:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:38:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:38:23: 1000000 INFO @ Wed, 22 Apr 2020 08:38:28: 2000000 INFO @ Wed, 22 Apr 2020 08:38:33: 3000000 INFO @ Wed, 22 Apr 2020 08:38:38: 4000000 INFO @ Wed, 22 Apr 2020 08:38:42: 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 08:38:47: 6000000 INFO @ Wed, 22 Apr 2020 08:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.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 08:38:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:38:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:38:52: 7000000 INFO @ Wed, 22 Apr 2020 08:38:54: 1000000 INFO @ Wed, 22 Apr 2020 08:38:58: 8000000 INFO @ Wed, 22 Apr 2020 08:39:00: 2000000 INFO @ Wed, 22 Apr 2020 08:39:03: 9000000 INFO @ Wed, 22 Apr 2020 08:39:05: 3000000 INFO @ Wed, 22 Apr 2020 08:39:08: 10000000 INFO @ Wed, 22 Apr 2020 08:39:10: 4000000 INFO @ Wed, 22 Apr 2020 08:39:14: 11000000 INFO @ Wed, 22 Apr 2020 08:39:16: 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 08:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.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 08:39:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:39:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:39:19: 12000000 INFO @ Wed, 22 Apr 2020 08:39:21: 6000000 INFO @ Wed, 22 Apr 2020 08:39:24: 1000000 INFO @ Wed, 22 Apr 2020 08:39:25: 13000000 INFO @ Wed, 22 Apr 2020 08:39:27: 7000000 INFO @ Wed, 22 Apr 2020 08:39:30: 2000000 INFO @ Wed, 22 Apr 2020 08:39:30: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:39:30: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:39:30: #1 total tags in treatment: 5912914 INFO @ Wed, 22 Apr 2020 08:39:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:39:30: #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 08:39:30: #1 tags after filtering in treatment: 4640451 INFO @ Wed, 22 Apr 2020 08:39:30: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Apr 2020 08:39:30: #1 finished! INFO @ Wed, 22 Apr 2020 08:39:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:39:30: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:39:30: Too few paired peaks (0) 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 08:39:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.05_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/SRX5883292/SRX5883292.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:39:32: 8000000 INFO @ Wed, 22 Apr 2020 08:39:35: 3000000 INFO @ Wed, 22 Apr 2020 08:39:38: 9000000 INFO @ Wed, 22 Apr 2020 08:39:41: 4000000 INFO @ Wed, 22 Apr 2020 08:39:43: 10000000 INFO @ Wed, 22 Apr 2020 08:39:47: 5000000 INFO @ Wed, 22 Apr 2020 08:39:49: 11000000 INFO @ Wed, 22 Apr 2020 08:39:52: 6000000 INFO @ Wed, 22 Apr 2020 08:39:55: 12000000 INFO @ Wed, 22 Apr 2020 08:39:58: 7000000 INFO @ Wed, 22 Apr 2020 08:40:00: 13000000 INFO @ Wed, 22 Apr 2020 08:40:03: 8000000 INFO @ Wed, 22 Apr 2020 08:40:05: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:40:05: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:40:05: #1 total tags in treatment: 5912914 INFO @ Wed, 22 Apr 2020 08:40:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:40:05: #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 08:40:05: #1 tags after filtering in treatment: 4640451 INFO @ Wed, 22 Apr 2020 08:40:05: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Apr 2020 08:40:05: #1 finished! INFO @ Wed, 22 Apr 2020 08:40:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:40:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:40:06: Too few paired peaks (0) 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 08:40:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.10_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/SRX5883292/SRX5883292.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:40:09: 9000000 INFO @ Wed, 22 Apr 2020 08:40:14: 10000000 INFO @ Wed, 22 Apr 2020 08:40:19: 11000000 INFO @ Wed, 22 Apr 2020 08:40:24: 12000000 INFO @ Wed, 22 Apr 2020 08:40:29: 13000000 INFO @ Wed, 22 Apr 2020 08:40:34: #1 tag size is determined as 38 bps INFO @ Wed, 22 Apr 2020 08:40:34: #1 tag size = 38 INFO @ Wed, 22 Apr 2020 08:40:34: #1 total tags in treatment: 5912914 INFO @ Wed, 22 Apr 2020 08:40:34: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:40:34: #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 08:40:34: #1 tags after filtering in treatment: 4640451 INFO @ Wed, 22 Apr 2020 08:40:34: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Apr 2020 08:40:34: #1 finished! INFO @ Wed, 22 Apr 2020 08:40:34: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:40:34: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 08:40:34: Too few paired peaks (0) 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 08:40:34: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.20_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/SRX5883292/SRX5883292.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5883292/SRX5883292.20_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。