Job ID = 5791801 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:45:41 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 ) 1900-01-00T00:00:00 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 : 10,229,482 reads read : 20,458,964 reads written : 20,458,964 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: 00:06:55 10229482 reads; of these: 10229482 (100.00%) were paired; of these: 2336779 (22.84%) aligned concordantly 0 times 6832909 (66.80%) aligned concordantly exactly 1 time 1059794 (10.36%) aligned concordantly >1 times ---- 2336779 pairs aligned concordantly 0 times; of these: 784919 (33.59%) aligned discordantly 1 time ---- 1551860 pairs aligned 0 times concordantly or discordantly; of these: 3103720 mates make up the pairs; of these: 2663079 (85.80%) aligned 0 times 183722 (5.92%) aligned exactly 1 time 256919 (8.28%) aligned >1 times 86.98% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 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] 1954640 / 8620712 = 0.2267 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 11:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.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 11:04:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:04:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:04:43: 1000000 INFO @ Wed, 22 Apr 2020 11:04:49: 2000000 INFO @ Wed, 22 Apr 2020 11:04:56: 3000000 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 11:05:02: 4000000 INFO @ Wed, 22 Apr 2020 11:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.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 11:05:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:05:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:05:09: 5000000 INFO @ Wed, 22 Apr 2020 11:05:11: 1000000 INFO @ Wed, 22 Apr 2020 11:05:16: 6000000 INFO @ Wed, 22 Apr 2020 11:05:17: 2000000 INFO @ Wed, 22 Apr 2020 11:05:23: 7000000 INFO @ Wed, 22 Apr 2020 11:05:23: 3000000 INFO @ Wed, 22 Apr 2020 11:05:29: 4000000 INFO @ Wed, 22 Apr 2020 11:05:30: 8000000 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 11:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.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 11:05:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:05:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:05:35: 5000000 INFO @ Wed, 22 Apr 2020 11:05:37: 9000000 INFO @ Wed, 22 Apr 2020 11:05:41: 1000000 INFO @ Wed, 22 Apr 2020 11:05:42: 6000000 INFO @ Wed, 22 Apr 2020 11:05:44: 10000000 INFO @ Wed, 22 Apr 2020 11:05:48: 7000000 INFO @ Wed, 22 Apr 2020 11:05:48: 2000000 INFO @ Wed, 22 Apr 2020 11:05:50: 11000000 INFO @ Wed, 22 Apr 2020 11:05:54: 8000000 INFO @ Wed, 22 Apr 2020 11:05:55: 3000000 INFO @ Wed, 22 Apr 2020 11:05:57: 12000000 INFO @ Wed, 22 Apr 2020 11:06:00: 9000000 INFO @ Wed, 22 Apr 2020 11:06:02: 4000000 INFO @ Wed, 22 Apr 2020 11:06:04: 13000000 INFO @ Wed, 22 Apr 2020 11:06:06: 10000000 INFO @ Wed, 22 Apr 2020 11:06:09: 5000000 INFO @ Wed, 22 Apr 2020 11:06:11: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:06:11: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:06:11: #1 total tags in treatment: 6098140 INFO @ Wed, 22 Apr 2020 11:06:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:06:11: #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 11:06:11: #1 tags after filtering in treatment: 3131849 INFO @ Wed, 22 Apr 2020 11:06:11: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 11:06:11: #1 finished! INFO @ Wed, 22 Apr 2020 11:06:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:06:11: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:06:11: 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 11:06:11: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:06:12: 11000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.05_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/SRX7756596/SRX7756596.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:06:16: 6000000 INFO @ Wed, 22 Apr 2020 11:06:18: 12000000 INFO @ Wed, 22 Apr 2020 11:06:23: 7000000 INFO @ Wed, 22 Apr 2020 11:06:24: 13000000 INFO @ Wed, 22 Apr 2020 11:06:29: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:06:29: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:06:29: #1 total tags in treatment: 6098140 INFO @ Wed, 22 Apr 2020 11:06:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:06:29: #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 11:06:29: #1 tags after filtering in treatment: 3131849 INFO @ Wed, 22 Apr 2020 11:06:29: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 11:06:29: #1 finished! INFO @ Wed, 22 Apr 2020 11:06:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:06:30: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:06:30: 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 11:06:30: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 11:06:30: 8000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.10_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/SRX7756596/SRX7756596.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:06:36: 9000000 INFO @ Wed, 22 Apr 2020 11:06:43: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:06:49: 11000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:06:56: 12000000 INFO @ Wed, 22 Apr 2020 11:07:02: 13000000 INFO @ Wed, 22 Apr 2020 11:07:08: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:07:08: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:07:08: #1 total tags in treatment: 6098140 INFO @ Wed, 22 Apr 2020 11:07:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:07:08: #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 11:07:08: #1 tags after filtering in treatment: 3131849 INFO @ Wed, 22 Apr 2020 11:07:08: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 11:07:08: #1 finished! INFO @ Wed, 22 Apr 2020 11:07:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:07:08: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:07:08: 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 11:07:08: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.20_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/SRX7756596/SRX7756596.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756596/SRX7756596.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling