Job ID = 5791189 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:57:12 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 ) 2020-04-22T00:01:26 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 : 20,154,345 reads read : 40,308,690 reads written : 40,308,690 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: 00:15:53 20154345 reads; of these: 20154345 (100.00%) were paired; of these: 5443657 (27.01%) aligned concordantly 0 times 10050984 (49.87%) aligned concordantly exactly 1 time 4659704 (23.12%) aligned concordantly >1 times ---- 5443657 pairs aligned concordantly 0 times; of these: 1113797 (20.46%) aligned discordantly 1 time ---- 4329860 pairs aligned 0 times concordantly or discordantly; of these: 8659720 mates make up the pairs; of these: 7738479 (89.36%) aligned 0 times 214463 (2.48%) aligned exactly 1 time 706778 (8.16%) aligned >1 times 80.80% overall alignment rate Time searching: 00:15:53 Overall time: 00:15:53 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 16 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] 5722631 / 15728321 = 0.3638 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 09:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.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 09:34:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:34:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:34:37: 1000000 INFO @ Wed, 22 Apr 2020 09:34:42: 2000000 INFO @ Wed, 22 Apr 2020 09:34:47: 3000000 INFO @ Wed, 22 Apr 2020 09:34:52: 4000000 INFO @ Wed, 22 Apr 2020 09:34:57: 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 09:35:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.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 09:35:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:35:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:35:02: 6000000 INFO @ Wed, 22 Apr 2020 09:35:07: 1000000 INFO @ Wed, 22 Apr 2020 09:35:07: 7000000 INFO @ Wed, 22 Apr 2020 09:35:12: 2000000 INFO @ Wed, 22 Apr 2020 09:35:13: 8000000 INFO @ Wed, 22 Apr 2020 09:35:17: 3000000 INFO @ Wed, 22 Apr 2020 09:35:18: 9000000 INFO @ Wed, 22 Apr 2020 09:35:22: 4000000 INFO @ Wed, 22 Apr 2020 09:35:23: 10000000 INFO @ Wed, 22 Apr 2020 09:35:28: 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 09:35:28: 11000000 INFO @ Wed, 22 Apr 2020 09:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.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 09:35:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:35:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:35:33: 6000000 INFO @ Wed, 22 Apr 2020 09:35:34: 12000000 INFO @ Wed, 22 Apr 2020 09:35:37: 1000000 INFO @ Wed, 22 Apr 2020 09:35:38: 7000000 INFO @ Wed, 22 Apr 2020 09:35:39: 13000000 INFO @ Wed, 22 Apr 2020 09:35:42: 2000000 INFO @ Wed, 22 Apr 2020 09:35:43: 8000000 INFO @ Wed, 22 Apr 2020 09:35:44: 14000000 INFO @ Wed, 22 Apr 2020 09:35:48: 3000000 INFO @ Wed, 22 Apr 2020 09:35:48: 9000000 INFO @ Wed, 22 Apr 2020 09:35:49: 15000000 INFO @ Wed, 22 Apr 2020 09:35:53: 4000000 INFO @ Wed, 22 Apr 2020 09:35:54: 10000000 INFO @ Wed, 22 Apr 2020 09:35:54: 16000000 INFO @ Wed, 22 Apr 2020 09:35:58: 5000000 INFO @ Wed, 22 Apr 2020 09:35:59: 11000000 INFO @ Wed, 22 Apr 2020 09:35:59: 17000000 INFO @ Wed, 22 Apr 2020 09:36:04: 6000000 INFO @ Wed, 22 Apr 2020 09:36:04: 12000000 INFO @ Wed, 22 Apr 2020 09:36:05: 18000000 INFO @ Wed, 22 Apr 2020 09:36:09: 7000000 INFO @ Wed, 22 Apr 2020 09:36:09: 13000000 INFO @ Wed, 22 Apr 2020 09:36:10: 19000000 INFO @ Wed, 22 Apr 2020 09:36:14: 8000000 INFO @ Wed, 22 Apr 2020 09:36:14: 14000000 INFO @ Wed, 22 Apr 2020 09:36:15: 20000000 INFO @ Wed, 22 Apr 2020 09:36:19: 9000000 INFO @ Wed, 22 Apr 2020 09:36:19: 15000000 INFO @ Wed, 22 Apr 2020 09:36:20: 21000000 INFO @ Wed, 22 Apr 2020 09:36:21: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:36:21: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:36:21: #1 total tags in treatment: 9181542 INFO @ Wed, 22 Apr 2020 09:36:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:36:21: #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 09:36:21: #1 tags after filtering in treatment: 4729942 INFO @ Wed, 22 Apr 2020 09:36:21: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 09:36:21: #1 finished! INFO @ Wed, 22 Apr 2020 09:36:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:36:22: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:36:22: 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 09:36:22: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:36:24: 10000000 INFO @ Wed, 22 Apr 2020 09:36:25: 16000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.05_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/SRX6614980/SRX6614980.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:36:30: 11000000 INFO @ Wed, 22 Apr 2020 09:36:30: 17000000 INFO @ Wed, 22 Apr 2020 09:36:35: 18000000 INFO @ Wed, 22 Apr 2020 09:36:35: 12000000 INFO @ Wed, 22 Apr 2020 09:36:40: 13000000 INFO @ Wed, 22 Apr 2020 09:36:40: 19000000 INFO @ Wed, 22 Apr 2020 09:36:45: 14000000 INFO @ Wed, 22 Apr 2020 09:36:45: 20000000 INFO @ Wed, 22 Apr 2020 09:36:51: 15000000 INFO @ Wed, 22 Apr 2020 09:36:51: 21000000 INFO @ Wed, 22 Apr 2020 09:36:51: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:36:51: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:36:51: #1 total tags in treatment: 9181542 INFO @ Wed, 22 Apr 2020 09:36:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:36:51: #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 09:36:52: #1 tags after filtering in treatment: 4729942 INFO @ Wed, 22 Apr 2020 09:36:52: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 09:36:52: #1 finished! INFO @ Wed, 22 Apr 2020 09:36:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:36:52: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:36:52: 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 09:36:52: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:36:56: 16000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.10_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/SRX6614980/SRX6614980.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:37:01: 17000000 INFO @ Wed, 22 Apr 2020 09:37:06: 18000000 INFO @ Wed, 22 Apr 2020 09:37:11: 19000000 INFO @ Wed, 22 Apr 2020 09:37:16: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:37:21: 21000000 INFO @ Wed, 22 Apr 2020 09:37:22: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:37:22: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:37:22: #1 total tags in treatment: 9181542 INFO @ Wed, 22 Apr 2020 09:37:22: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:37:22: #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 09:37:22: #1 tags after filtering in treatment: 4729942 INFO @ Wed, 22 Apr 2020 09:37:22: #1 Redundant rate of treatment: 0.48 INFO @ Wed, 22 Apr 2020 09:37:22: #1 finished! INFO @ Wed, 22 Apr 2020 09:37:22: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:37:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:37:23: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 09:37:23: 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 09:37:23: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.20_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/SRX6614980/SRX6614980.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614980/SRX6614980.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。