Job ID = 5791673 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:20:15 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 ) 2020-04-22T01:20:15 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 ) 2020-04-22T01:20:15 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 ) 2020-04-22T01:21:28 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 17,557,466 reads read : 35,114,932 reads written : 35,114,932 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: 00:19:05 17557466 reads; of these: 17557466 (100.00%) were paired; of these: 5563703 (31.69%) aligned concordantly 0 times 9841183 (56.05%) aligned concordantly exactly 1 time 2152580 (12.26%) aligned concordantly >1 times ---- 5563703 pairs aligned concordantly 0 times; of these: 1319498 (23.72%) aligned discordantly 1 time ---- 4244205 pairs aligned 0 times concordantly or discordantly; of these: 8488410 mates make up the pairs; of these: 7407419 (87.27%) aligned 0 times 355639 (4.19%) aligned exactly 1 time 725352 (8.55%) aligned >1 times 78.91% overall alignment rate Time searching: 00:19:05 Overall time: 00:19:05 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 24 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] 2290085 / 13246936 = 0.1729 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 11:27:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.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 11:27:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:27:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:27:45: 1000000 INFO @ Wed, 22 Apr 2020 11:27:52: 2000000 INFO @ Wed, 22 Apr 2020 11:27:59: 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 11:28:07: 4000000 INFO @ Wed, 22 Apr 2020 11:28:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.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 11:28:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:28:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:28:15: 5000000 INFO @ Wed, 22 Apr 2020 11:28:16: 1000000 INFO @ Wed, 22 Apr 2020 11:28:23: 6000000 INFO @ Wed, 22 Apr 2020 11:28:25: 2000000 INFO @ Wed, 22 Apr 2020 11:28:31: 7000000 INFO @ Wed, 22 Apr 2020 11:28:34: 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 11:28:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.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 11:28:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 11:28:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 11:28:40: 8000000 INFO @ Wed, 22 Apr 2020 11:28:44: 4000000 INFO @ Wed, 22 Apr 2020 11:28:48: 1000000 INFO @ Wed, 22 Apr 2020 11:28:49: 9000000 INFO @ Wed, 22 Apr 2020 11:28:53: 5000000 INFO @ Wed, 22 Apr 2020 11:28:58: 10000000 INFO @ Wed, 22 Apr 2020 11:28:58: 2000000 INFO @ Wed, 22 Apr 2020 11:29:03: 6000000 INFO @ Wed, 22 Apr 2020 11:29:07: 11000000 INFO @ Wed, 22 Apr 2020 11:29:09: 3000000 INFO @ Wed, 22 Apr 2020 11:29:13: 7000000 INFO @ Wed, 22 Apr 2020 11:29:16: 12000000 INFO @ Wed, 22 Apr 2020 11:29:19: 4000000 INFO @ Wed, 22 Apr 2020 11:29:23: 8000000 INFO @ Wed, 22 Apr 2020 11:29:25: 13000000 INFO @ Wed, 22 Apr 2020 11:29:30: 5000000 INFO @ Wed, 22 Apr 2020 11:29:33: 9000000 INFO @ Wed, 22 Apr 2020 11:29:34: 14000000 INFO @ Wed, 22 Apr 2020 11:29:41: 6000000 INFO @ Wed, 22 Apr 2020 11:29:43: 15000000 INFO @ Wed, 22 Apr 2020 11:29:43: 10000000 INFO @ Wed, 22 Apr 2020 11:29:51: 7000000 INFO @ Wed, 22 Apr 2020 11:29:52: 16000000 INFO @ Wed, 22 Apr 2020 11:29:53: 11000000 INFO @ Wed, 22 Apr 2020 11:30:01: 17000000 INFO @ Wed, 22 Apr 2020 11:30:02: 8000000 INFO @ Wed, 22 Apr 2020 11:30:03: 12000000 INFO @ Wed, 22 Apr 2020 11:30:10: 18000000 INFO @ Wed, 22 Apr 2020 11:30:12: 9000000 INFO @ Wed, 22 Apr 2020 11:30:12: 13000000 INFO @ Wed, 22 Apr 2020 11:30:19: 19000000 INFO @ Wed, 22 Apr 2020 11:30:22: 14000000 INFO @ Wed, 22 Apr 2020 11:30:23: 10000000 INFO @ Wed, 22 Apr 2020 11:30:29: 20000000 INFO @ Wed, 22 Apr 2020 11:30:32: 15000000 INFO @ Wed, 22 Apr 2020 11:30:34: 11000000 INFO @ Wed, 22 Apr 2020 11:30:38: 21000000 INFO @ Wed, 22 Apr 2020 11:30:42: 16000000 INFO @ Wed, 22 Apr 2020 11:30:44: 12000000 INFO @ Wed, 22 Apr 2020 11:30:47: 22000000 INFO @ Wed, 22 Apr 2020 11:30:51: 17000000 INFO @ Wed, 22 Apr 2020 11:30:55: 13000000 INFO @ Wed, 22 Apr 2020 11:30:56: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 11:30:58: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:30:58: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:30:58: #1 total tags in treatment: 9856458 INFO @ Wed, 22 Apr 2020 11:30:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:30:58: #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 11:30:58: #1 tags after filtering in treatment: 7102214 INFO @ Wed, 22 Apr 2020 11:30:58: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 11:30:58: #1 finished! INFO @ Wed, 22 Apr 2020 11:30:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:30:58: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:30:58: 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 11:30:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.05_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/SRX7409634/SRX7409634.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:31:01: 18000000 INFO @ Wed, 22 Apr 2020 11:31:06: 14000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 11:31:10: 19000000 INFO @ Wed, 22 Apr 2020 11:31:17: 15000000 INFO @ Wed, 22 Apr 2020 11:31:19: 20000000 INFO @ Wed, 22 Apr 2020 11:31:27: 16000000 INFO @ Wed, 22 Apr 2020 11:31:28: 21000000 INFO @ Wed, 22 Apr 2020 11:31:37: 22000000 INFO @ Wed, 22 Apr 2020 11:31:38: 17000000 INFO @ Wed, 22 Apr 2020 11:31:46: 23000000 INFO @ Wed, 22 Apr 2020 11:31:47: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:31:47: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:31:47: #1 total tags in treatment: 9856458 INFO @ Wed, 22 Apr 2020 11:31:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:31:47: #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 11:31:48: #1 tags after filtering in treatment: 7102214 INFO @ Wed, 22 Apr 2020 11:31:48: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 11:31:48: #1 finished! INFO @ Wed, 22 Apr 2020 11:31:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:31:48: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:31:48: 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 11:31:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.10_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/SRX7409634/SRX7409634.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 11:31:49: 18000000 INFO @ Wed, 22 Apr 2020 11:31:59: 19000000 INFO @ Wed, 22 Apr 2020 11:32:09: 20000000 INFO @ Wed, 22 Apr 2020 11:32:18: 21000000 INFO @ Wed, 22 Apr 2020 11:32:28: 22000000 INFO @ Wed, 22 Apr 2020 11:32:38: 23000000 INFO @ Wed, 22 Apr 2020 11:32:39: #1 tag size is determined as 150 bps INFO @ Wed, 22 Apr 2020 11:32:39: #1 tag size = 150 INFO @ Wed, 22 Apr 2020 11:32:39: #1 total tags in treatment: 9856458 INFO @ Wed, 22 Apr 2020 11:32:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 11:32:39: #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 11:32:39: #1 tags after filtering in treatment: 7102214 INFO @ Wed, 22 Apr 2020 11:32:39: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 22 Apr 2020 11:32:39: #1 finished! INFO @ Wed, 22 Apr 2020 11:32:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 11:32:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 11:32:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 11:32:40: 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 11:32:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.20_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/SRX7409634/SRX7409634.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409634/SRX7409634.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling