Job ID = 5791202 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:55:49 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 ) 2020-04-22T00:00:57 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 ) 2020-04-22T00:00:57 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 ) 2020-04-22T00:00:57 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 ) 2020-04-22T00:02:57 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 : 17,230,687 reads read : 34,461,374 reads written : 34,461,374 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: 00:14:11 17230687 reads; of these: 17230687 (100.00%) were paired; of these: 4333280 (25.15%) aligned concordantly 0 times 8621929 (50.04%) aligned concordantly exactly 1 time 4275478 (24.81%) aligned concordantly >1 times ---- 4333280 pairs aligned concordantly 0 times; of these: 954773 (22.03%) aligned discordantly 1 time ---- 3378507 pairs aligned 0 times concordantly or discordantly; of these: 6757014 mates make up the pairs; of these: 5550116 (82.14%) aligned 0 times 209224 (3.10%) aligned exactly 1 time 997674 (14.77%) aligned >1 times 83.89% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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 12 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] 4682152 / 13737310 = 0.3408 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 09:37:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.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 09:37:33: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:37:33: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:37:39: 1000000 INFO @ Wed, 22 Apr 2020 09:37:46: 2000000 INFO @ Wed, 22 Apr 2020 09:37:55: 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 09:38:03: 4000000 INFO @ Wed, 22 Apr 2020 09:38:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.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 09:38:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:38:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:38:09: 1000000 INFO @ Wed, 22 Apr 2020 09:38:11: 5000000 INFO @ Wed, 22 Apr 2020 09:38:15: 2000000 INFO @ Wed, 22 Apr 2020 09:38:19: 6000000 INFO @ Wed, 22 Apr 2020 09:38:20: 3000000 INFO @ Wed, 22 Apr 2020 09:38:26: 4000000 INFO @ Wed, 22 Apr 2020 09:38:28: 7000000 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 09:38:32: 5000000 INFO @ Wed, 22 Apr 2020 09:38:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.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 09:38:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:38:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:38:36: 8000000 INFO @ Wed, 22 Apr 2020 09:38:37: 6000000 INFO @ Wed, 22 Apr 2020 09:38:40: 1000000 INFO @ Wed, 22 Apr 2020 09:38:43: 7000000 INFO @ Wed, 22 Apr 2020 09:38:44: 9000000 INFO @ Wed, 22 Apr 2020 09:38:45: 2000000 INFO @ Wed, 22 Apr 2020 09:38:48: 8000000 INFO @ Wed, 22 Apr 2020 09:38:50: 10000000 INFO @ Wed, 22 Apr 2020 09:38:51: 3000000 INFO @ Wed, 22 Apr 2020 09:38:54: 9000000 INFO @ Wed, 22 Apr 2020 09:38:56: 11000000 INFO @ Wed, 22 Apr 2020 09:38:56: 4000000 INFO @ Wed, 22 Apr 2020 09:38:59: 10000000 INFO @ Wed, 22 Apr 2020 09:39:01: 12000000 INFO @ Wed, 22 Apr 2020 09:39:02: 5000000 INFO @ Wed, 22 Apr 2020 09:39:05: 11000000 INFO @ Wed, 22 Apr 2020 09:39:06: 13000000 INFO @ Wed, 22 Apr 2020 09:39:07: 6000000 INFO @ Wed, 22 Apr 2020 09:39:10: 12000000 INFO @ Wed, 22 Apr 2020 09:39:12: 14000000 INFO @ Wed, 22 Apr 2020 09:39:13: 7000000 INFO @ Wed, 22 Apr 2020 09:39:16: 13000000 INFO @ Wed, 22 Apr 2020 09:39:18: 15000000 INFO @ Wed, 22 Apr 2020 09:39:18: 8000000 INFO @ Wed, 22 Apr 2020 09:39:21: 14000000 INFO @ Wed, 22 Apr 2020 09:39:23: 16000000 INFO @ Wed, 22 Apr 2020 09:39:24: 9000000 INFO @ Wed, 22 Apr 2020 09:39:27: 15000000 INFO @ Wed, 22 Apr 2020 09:39:29: 10000000 INFO @ Wed, 22 Apr 2020 09:39:29: 17000000 INFO @ Wed, 22 Apr 2020 09:39:32: 16000000 INFO @ Wed, 22 Apr 2020 09:39:35: 11000000 INFO @ Wed, 22 Apr 2020 09:39:35: 18000000 INFO @ Wed, 22 Apr 2020 09:39:38: 17000000 INFO @ Wed, 22 Apr 2020 09:39:40: 12000000 INFO @ Wed, 22 Apr 2020 09:39:41: 19000000 INFO @ Wed, 22 Apr 2020 09:39:43: 18000000 INFO @ Wed, 22 Apr 2020 09:39:44: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:39:44: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:39:44: #1 total tags in treatment: 8368078 INFO @ Wed, 22 Apr 2020 09:39:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:39:44: #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 09:39:44: #1 tags after filtering in treatment: 4508290 INFO @ Wed, 22 Apr 2020 09:39:44: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 09:39:44: #1 finished! INFO @ Wed, 22 Apr 2020 09:39:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:39:44: #2 number of paired peaks: 8 WARNING @ Wed, 22 Apr 2020 09:39:44: Too few paired peaks (8) 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 09:39:44: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 09:39:45: 13000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.05_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/SRX6614991/SRX6614991.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:39:49: 19000000 INFO @ Wed, 22 Apr 2020 09:39:51: 14000000 INFO @ Wed, 22 Apr 2020 09:39:52: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:39:52: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:39:52: #1 total tags in treatment: 8368078 INFO @ Wed, 22 Apr 2020 09:39:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:39:52: #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 09:39:52: #1 tags after filtering in treatment: 4508290 INFO @ Wed, 22 Apr 2020 09:39:52: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 09:39:52: #1 finished! INFO @ Wed, 22 Apr 2020 09:39:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:39:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:39:52: #2 number of paired peaks: 8 WARNING @ Wed, 22 Apr 2020 09:39:52: Too few paired peaks (8) 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 09:39:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.10_peaks.narrowPeak: No such file or directory INFO @ Wed, 22 Apr 2020 09:39:56: 15000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:40:01: 16000000 INFO @ Wed, 22 Apr 2020 09:40:07: 17000000 INFO @ Wed, 22 Apr 2020 09:40:12: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:40:17: 19000000 INFO @ Wed, 22 Apr 2020 09:40:21: #1 tag size is determined as 101 bps INFO @ Wed, 22 Apr 2020 09:40:21: #1 tag size = 101 INFO @ Wed, 22 Apr 2020 09:40:21: #1 total tags in treatment: 8368078 INFO @ Wed, 22 Apr 2020 09:40:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:40:21: #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 09:40:21: #1 tags after filtering in treatment: 4508290 INFO @ Wed, 22 Apr 2020 09:40:21: #1 Redundant rate of treatment: 0.46 INFO @ Wed, 22 Apr 2020 09:40:21: #1 finished! INFO @ Wed, 22 Apr 2020 09:40:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:40:21: #2 number of paired peaks: 8 WARNING @ Wed, 22 Apr 2020 09:40:21: Too few paired peaks (8) 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 09:40:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.20_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/SRX6614991/SRX6614991.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6614991/SRX6614991.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。