Job ID = 5791813 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:42:39 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 ) 2020-04-22T01:42:39 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 ) 2020-04-22T01:55:46 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 ) 2020-04-22T01:58:03 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 ) 2020-04-22T01:58:03 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 : 18,345,041 reads read : 36,690,082 reads written : 36,690,082 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: 00:00:01 Multiseed full-index search: 00:16:11 18345041 reads; of these: 18345041 (100.00%) were paired; of these: 4769868 (26.00%) aligned concordantly 0 times 11479315 (62.57%) aligned concordantly exactly 1 time 2095858 (11.42%) aligned concordantly >1 times ---- 4769868 pairs aligned concordantly 0 times; of these: 1311708 (27.50%) aligned discordantly 1 time ---- 3458160 pairs aligned 0 times concordantly or discordantly; of these: 6916320 mates make up the pairs; of these: 6040090 (87.33%) aligned 0 times 355663 (5.14%) aligned exactly 1 time 520567 (7.53%) aligned >1 times 83.54% overall alignment rate Time searching: 00:16:12 Overall time: 00:16:12 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_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] 2951280 / 14782620 = 0.1996 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 11:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.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 11:27:03: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:27:03: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:27:09: 1000000 INFO @ Wed, 22 Apr 2020 11:27:16: 2000000 INFO @ Wed, 22 Apr 2020 11:27:23: 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 11:27:30: 4000000 INFO @ Wed, 22 Apr 2020 11:27:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.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 11:27:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:27:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:27:37: 5000000 INFO @ Wed, 22 Apr 2020 11:27:40: 1000000 INFO @ Wed, 22 Apr 2020 11:27:45: 6000000 INFO @ Wed, 22 Apr 2020 11:27:47: 2000000 INFO @ Wed, 22 Apr 2020 11:27:52: 7000000 INFO @ Wed, 22 Apr 2020 11:27:55: 3000000 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 11:28:00: 8000000 INFO @ Wed, 22 Apr 2020 11:28:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.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 11:28:02: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:28:02: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:28:03: 4000000 INFO @ Wed, 22 Apr 2020 11:28:08: 9000000 INFO @ Wed, 22 Apr 2020 11:28:10: 1000000 INFO @ Wed, 22 Apr 2020 11:28:11: 5000000 INFO @ Wed, 22 Apr 2020 11:28:16: 10000000 INFO @ Wed, 22 Apr 2020 11:28:19: 2000000 INFO @ Wed, 22 Apr 2020 11:28:19: 6000000 INFO @ Wed, 22 Apr 2020 11:28:24: 11000000 INFO @ Wed, 22 Apr 2020 11:28:28: 3000000 INFO @ Wed, 22 Apr 2020 11:28:28: 7000000 INFO @ Wed, 22 Apr 2020 11:28:33: 12000000 INFO @ Wed, 22 Apr 2020 11:28:36: 8000000 INFO @ Wed, 22 Apr 2020 11:28:36: 4000000 INFO @ Wed, 22 Apr 2020 11:28:41: 13000000 INFO @ Wed, 22 Apr 2020 11:28:44: 9000000 INFO @ Wed, 22 Apr 2020 11:28:45: 5000000 INFO @ Wed, 22 Apr 2020 11:28:49: 14000000 INFO @ Wed, 22 Apr 2020 11:28:53: 10000000 INFO @ Wed, 22 Apr 2020 11:28:53: 6000000 INFO @ Wed, 22 Apr 2020 11:28:58: 15000000 INFO @ Wed, 22 Apr 2020 11:29:01: 11000000 INFO @ Wed, 22 Apr 2020 11:29:02: 7000000 INFO @ Wed, 22 Apr 2020 11:29:06: 16000000 INFO @ Wed, 22 Apr 2020 11:29:09: 8000000 INFO @ Wed, 22 Apr 2020 11:29:10: 12000000 INFO @ Wed, 22 Apr 2020 11:29:15: 17000000 INFO @ Wed, 22 Apr 2020 11:29:17: 13000000 INFO @ Wed, 22 Apr 2020 11:29:17: 9000000 INFO @ Wed, 22 Apr 2020 11:29:22: 18000000 INFO @ Wed, 22 Apr 2020 11:29:24: 10000000 INFO @ Wed, 22 Apr 2020 11:29:25: 14000000 INFO @ Wed, 22 Apr 2020 11:29:29: 19000000 INFO @ Wed, 22 Apr 2020 11:29:31: 11000000 INFO @ Wed, 22 Apr 2020 11:29:32: 15000000 INFO @ Wed, 22 Apr 2020 11:29:36: 20000000 INFO @ Wed, 22 Apr 2020 11:29:38: 12000000 INFO @ Wed, 22 Apr 2020 11:29:39: 16000000 INFO @ Wed, 22 Apr 2020 11:29:43: 21000000 INFO @ Wed, 22 Apr 2020 11:29:45: 13000000 INFO @ Wed, 22 Apr 2020 11:29:46: 17000000 INFO @ Wed, 22 Apr 2020 11:29:50: 22000000 INFO @ Wed, 22 Apr 2020 11:29:53: 14000000 INFO @ Wed, 22 Apr 2020 11:29:54: 18000000 INFO @ Wed, 22 Apr 2020 11:29:57: 23000000 INFO @ Wed, 22 Apr 2020 11:30:00: 15000000 INFO @ Wed, 22 Apr 2020 11:30:02: 19000000 INFO @ Wed, 22 Apr 2020 11:30:04: 24000000 INFO @ Wed, 22 Apr 2020 11:30:07: 16000000 INFO @ Wed, 22 Apr 2020 11:30:09: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:30:09: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:30:09: #1 total tags in treatment: 10839789 INFO @ Wed, 22 Apr 2020 11:30:09: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:30:09: #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 11:30:09: #1 tags after filtering in treatment: 5016508 INFO @ Wed, 22 Apr 2020 11:30:09: #1 Redundant rate of treatment: 0.54 INFO @ Wed, 22 Apr 2020 11:30:09: #1 finished! INFO @ Wed, 22 Apr 2020 11:30:09: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:30:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:30:09: 20000000 INFO @ Wed, 22 Apr 2020 11:30:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:30:09: 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 11:30:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:30:14: 17000000 INFO @ Wed, 22 Apr 2020 11:30:17: 21000000 INFO @ Wed, 22 Apr 2020 11:30:22: 18000000 INFO @ Wed, 22 Apr 2020 11:30:24: 22000000 INFO @ Wed, 22 Apr 2020 11:30:28: 19000000 INFO @ Wed, 22 Apr 2020 11:30:31: 23000000 INFO @ Wed, 22 Apr 2020 11:30:35: 20000000 INFO @ Wed, 22 Apr 2020 11:30:38: 24000000 INFO @ Wed, 22 Apr 2020 11:30:42: 21000000 INFO @ Wed, 22 Apr 2020 11:30:43: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:30:43: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:30:43: #1 total tags in treatment: 10839789 INFO @ Wed, 22 Apr 2020 11:30:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:30:43: #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 11:30:43: #1 tags after filtering in treatment: 5016508 INFO @ Wed, 22 Apr 2020 11:30:43: #1 Redundant rate of treatment: 0.54 INFO @ Wed, 22 Apr 2020 11:30:43: #1 finished! INFO @ Wed, 22 Apr 2020 11:30:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:30:43: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:30:43: 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 11:30:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.10_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/SRX7756598/SRX7756598.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:30:48: 22000000 INFO @ Wed, 22 Apr 2020 11:30:54: 23000000 INFO @ Wed, 22 Apr 2020 11:31:00: 24000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:31:05: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 11:31:05: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 11:31:05: #1 total tags in treatment: 10839789 INFO @ Wed, 22 Apr 2020 11:31:05: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:31:05: #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 11:31:05: #1 tags after filtering in treatment: 5016508 INFO @ Wed, 22 Apr 2020 11:31:05: #1 Redundant rate of treatment: 0.54 INFO @ Wed, 22 Apr 2020 11:31:05: #1 finished! INFO @ Wed, 22 Apr 2020 11:31:05: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:31:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:31:06: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:31:06: 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 11:31:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.20_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/SRX7756598/SRX7756598.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7756598/SRX7756598.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling