Job ID = 5791646 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:08:00 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 : 28,328,470 reads read : 56,656,940 reads written : 56,656,940 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: 00:14:42 28328470 reads; of these: 28328470 (100.00%) were paired; of these: 620584 (2.19%) aligned concordantly 0 times 25353084 (89.50%) aligned concordantly exactly 1 time 2354802 (8.31%) aligned concordantly >1 times ---- 620584 pairs aligned concordantly 0 times; of these: 38091 (6.14%) aligned discordantly 1 time ---- 582493 pairs aligned 0 times concordantly or discordantly; of these: 1164986 mates make up the pairs; of these: 954708 (81.95%) aligned 0 times 176063 (15.11%) aligned exactly 1 time 34215 (2.94%) aligned >1 times 98.31% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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] 3923310 / 27717776 = 0.1415 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 10:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.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 10:42:43: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:43: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:48: 1000000 INFO @ Wed, 22 Apr 2020 10:42:53: 2000000 INFO @ Wed, 22 Apr 2020 10:42:58: 3000000 INFO @ Wed, 22 Apr 2020 10:43:02: 4000000 INFO @ Wed, 22 Apr 2020 10:43:07: 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 10:43:12: 6000000 INFO @ Wed, 22 Apr 2020 10:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.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 10:43:12: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:12: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:17: 1000000 INFO @ Wed, 22 Apr 2020 10:43:17: 7000000 INFO @ Wed, 22 Apr 2020 10:43:22: 2000000 INFO @ Wed, 22 Apr 2020 10:43:22: 8000000 INFO @ Wed, 22 Apr 2020 10:43:26: 3000000 INFO @ Wed, 22 Apr 2020 10:43:27: 9000000 INFO @ Wed, 22 Apr 2020 10:43:30: 4000000 INFO @ Wed, 22 Apr 2020 10:43:32: 10000000 INFO @ Wed, 22 Apr 2020 10:43:35: 5000000 INFO @ Wed, 22 Apr 2020 10:43:38: 11000000 INFO @ Wed, 22 Apr 2020 10:43:39: 6000000 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 10:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.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 10:43:42: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:43:42: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:43: 12000000 INFO @ Wed, 22 Apr 2020 10:43:44: 7000000 INFO @ Wed, 22 Apr 2020 10:43:47: 1000000 INFO @ Wed, 22 Apr 2020 10:43:48: 13000000 INFO @ Wed, 22 Apr 2020 10:43:48: 8000000 INFO @ Wed, 22 Apr 2020 10:43:52: 2000000 INFO @ Wed, 22 Apr 2020 10:43:53: 9000000 INFO @ Wed, 22 Apr 2020 10:43:53: 14000000 INFO @ Wed, 22 Apr 2020 10:43:56: 3000000 INFO @ Wed, 22 Apr 2020 10:43:57: 10000000 INFO @ Wed, 22 Apr 2020 10:43:58: 15000000 INFO @ Wed, 22 Apr 2020 10:44:01: 4000000 INFO @ Wed, 22 Apr 2020 10:44:02: 11000000 INFO @ Wed, 22 Apr 2020 10:44:03: 16000000 INFO @ Wed, 22 Apr 2020 10:44:05: 5000000 INFO @ Wed, 22 Apr 2020 10:44:06: 12000000 INFO @ Wed, 22 Apr 2020 10:44:08: 17000000 INFO @ Wed, 22 Apr 2020 10:44:10: 6000000 INFO @ Wed, 22 Apr 2020 10:44:10: 13000000 INFO @ Wed, 22 Apr 2020 10:44:13: 18000000 INFO @ Wed, 22 Apr 2020 10:44:14: 7000000 INFO @ Wed, 22 Apr 2020 10:44:14: 14000000 INFO @ Wed, 22 Apr 2020 10:44:18: 19000000 INFO @ Wed, 22 Apr 2020 10:44:18: 8000000 INFO @ Wed, 22 Apr 2020 10:44:19: 15000000 INFO @ Wed, 22 Apr 2020 10:44:23: 20000000 INFO @ Wed, 22 Apr 2020 10:44:23: 9000000 INFO @ Wed, 22 Apr 2020 10:44:23: 16000000 INFO @ Wed, 22 Apr 2020 10:44:28: 17000000 INFO @ Wed, 22 Apr 2020 10:44:28: 10000000 INFO @ Wed, 22 Apr 2020 10:44:28: 21000000 INFO @ Wed, 22 Apr 2020 10:44:32: 18000000 INFO @ Wed, 22 Apr 2020 10:44:32: 11000000 INFO @ Wed, 22 Apr 2020 10:44:33: 22000000 INFO @ Wed, 22 Apr 2020 10:44:36: 19000000 INFO @ Wed, 22 Apr 2020 10:44:37: 12000000 INFO @ Wed, 22 Apr 2020 10:44:38: 23000000 INFO @ Wed, 22 Apr 2020 10:44:40: 20000000 INFO @ Wed, 22 Apr 2020 10:44:41: 13000000 INFO @ Wed, 22 Apr 2020 10:44:43: 24000000 INFO @ Wed, 22 Apr 2020 10:44:44: 21000000 INFO @ Wed, 22 Apr 2020 10:44:46: 14000000 INFO @ Wed, 22 Apr 2020 10:44:48: 25000000 INFO @ Wed, 22 Apr 2020 10:44:48: 22000000 INFO @ Wed, 22 Apr 2020 10:44:50: 15000000 INFO @ Wed, 22 Apr 2020 10:44:52: 23000000 INFO @ Wed, 22 Apr 2020 10:44:53: 26000000 INFO @ Wed, 22 Apr 2020 10:44:54: 16000000 INFO @ Wed, 22 Apr 2020 10:44:57: 24000000 INFO @ Wed, 22 Apr 2020 10:44:58: 27000000 INFO @ Wed, 22 Apr 2020 10:44:58: 17000000 INFO @ Wed, 22 Apr 2020 10:45:01: 25000000 INFO @ Wed, 22 Apr 2020 10:45:02: 18000000 INFO @ Wed, 22 Apr 2020 10:45:03: 28000000 INFO @ Wed, 22 Apr 2020 10:45:05: 26000000 INFO @ Wed, 22 Apr 2020 10:45:07: 19000000 INFO @ Wed, 22 Apr 2020 10:45:08: 29000000 INFO @ Wed, 22 Apr 2020 10:45:09: 27000000 INFO @ Wed, 22 Apr 2020 10:45:11: 20000000 INFO @ Wed, 22 Apr 2020 10:45:13: 30000000 INFO @ Wed, 22 Apr 2020 10:45:14: 28000000 INFO @ Wed, 22 Apr 2020 10:45:15: 21000000 INFO @ Wed, 22 Apr 2020 10:45:17: 31000000 INFO @ Wed, 22 Apr 2020 10:45:18: 29000000 INFO @ Wed, 22 Apr 2020 10:45:19: 22000000 INFO @ Wed, 22 Apr 2020 10:45:22: 30000000 INFO @ Wed, 22 Apr 2020 10:45:22: 32000000 INFO @ Wed, 22 Apr 2020 10:45:23: 23000000 INFO @ Wed, 22 Apr 2020 10:45:26: 31000000 INFO @ Wed, 22 Apr 2020 10:45:27: 33000000 INFO @ Wed, 22 Apr 2020 10:45:28: 24000000 INFO @ Wed, 22 Apr 2020 10:45:31: 32000000 INFO @ Wed, 22 Apr 2020 10:45:32: 25000000 INFO @ Wed, 22 Apr 2020 10:45:32: 34000000 INFO @ Wed, 22 Apr 2020 10:45:35: 33000000 INFO @ Wed, 22 Apr 2020 10:45:36: 26000000 INFO @ Wed, 22 Apr 2020 10:45:37: 35000000 INFO @ Wed, 22 Apr 2020 10:45:39: 34000000 INFO @ Wed, 22 Apr 2020 10:45:40: 27000000 INFO @ Wed, 22 Apr 2020 10:45:42: 36000000 INFO @ Wed, 22 Apr 2020 10:45:44: 35000000 INFO @ Wed, 22 Apr 2020 10:45:44: 28000000 INFO @ Wed, 22 Apr 2020 10:45:47: 37000000 INFO @ Wed, 22 Apr 2020 10:45:48: 36000000 INFO @ Wed, 22 Apr 2020 10:45:49: 29000000 INFO @ Wed, 22 Apr 2020 10:45:52: 38000000 INFO @ Wed, 22 Apr 2020 10:45:52: 37000000 INFO @ Wed, 22 Apr 2020 10:45:53: 30000000 INFO @ Wed, 22 Apr 2020 10:45:57: 38000000 INFO @ Wed, 22 Apr 2020 10:45:57: 31000000 INFO @ Wed, 22 Apr 2020 10:45:57: 39000000 INFO @ Wed, 22 Apr 2020 10:46:01: 39000000 INFO @ Wed, 22 Apr 2020 10:46:01: 32000000 INFO @ Wed, 22 Apr 2020 10:46:02: 40000000 INFO @ Wed, 22 Apr 2020 10:46:05: 40000000 INFO @ Wed, 22 Apr 2020 10:46:05: 33000000 INFO @ Wed, 22 Apr 2020 10:46:07: 41000000 INFO @ Wed, 22 Apr 2020 10:46:09: 34000000 INFO @ Wed, 22 Apr 2020 10:46:09: 41000000 INFO @ Wed, 22 Apr 2020 10:46:12: 42000000 INFO @ Wed, 22 Apr 2020 10:46:13: 35000000 INFO @ Wed, 22 Apr 2020 10:46:14: 42000000 INFO @ Wed, 22 Apr 2020 10:46:17: 43000000 INFO @ Wed, 22 Apr 2020 10:46:18: 36000000 INFO @ Wed, 22 Apr 2020 10:46:18: 43000000 INFO @ Wed, 22 Apr 2020 10:46:22: 37000000 INFO @ Wed, 22 Apr 2020 10:46:23: 44000000 INFO @ Wed, 22 Apr 2020 10:46:23: 44000000 INFO @ Wed, 22 Apr 2020 10:46:26: 38000000 INFO @ Wed, 22 Apr 2020 10:46:28: 45000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:46:28: 45000000 INFO @ Wed, 22 Apr 2020 10:46:30: 39000000 INFO @ Wed, 22 Apr 2020 10:46:33: 46000000 INFO @ Wed, 22 Apr 2020 10:46:34: 46000000 INFO @ Wed, 22 Apr 2020 10:46:35: 40000000 INFO @ Wed, 22 Apr 2020 10:46:38: 47000000 INFO @ Wed, 22 Apr 2020 10:46:39: 47000000 INFO @ Wed, 22 Apr 2020 10:46:39: 41000000 INFO @ Wed, 22 Apr 2020 10:46:42: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:46:42: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:46:42: #1 total tags in treatment: 23786112 INFO @ Wed, 22 Apr 2020 10:46:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:42: #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 10:46:43: #1 tags after filtering in treatment: 12229703 INFO @ Wed, 22 Apr 2020 10:46:43: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 10:46:43: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:43: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:43: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:46:43: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:46:43: #1 total tags in treatment: 23786112 INFO @ Wed, 22 Apr 2020 10:46:43: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:43: #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 10:46:43: 42000000 INFO @ Wed, 22 Apr 2020 10:46:43: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:46:43: 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 10:46:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.05_peaks.narrowPeak: No such file or directory INFO @ Wed, 22 Apr 2020 10:46:44: #1 tags after filtering in treatment: 12229703 INFO @ Wed, 22 Apr 2020 10:46:44: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 10:46:44: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:44: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:46:44: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:46:44: 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 10:46:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.10_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/SRX7409610/SRX7409610.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:46:47: 43000000 INFO @ Wed, 22 Apr 2020 10:46:51: 44000000 INFO @ Wed, 22 Apr 2020 10:46:56: 45000000 INFO @ Wed, 22 Apr 2020 10:47:00: 46000000 INFO @ Wed, 22 Apr 2020 10:47:04: 47000000 INFO @ Wed, 22 Apr 2020 10:47:08: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:47:08: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:47:08: #1 total tags in treatment: 23786112 INFO @ Wed, 22 Apr 2020 10:47:08: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:47:08: #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 10:47:08: #1 tags after filtering in treatment: 12229703 INFO @ Wed, 22 Apr 2020 10:47:08: #1 Redundant rate of treatment: 0.49 INFO @ Wed, 22 Apr 2020 10:47:08: #1 finished! INFO @ Wed, 22 Apr 2020 10:47:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:47:09: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:47:09: 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 10:47:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.20_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/SRX7409610/SRX7409610.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409610/SRX7409610.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling