Job ID = 5791648 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T01:14:01 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 : 22,335,892 reads read : 44,671,784 reads written : 44,671,784 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: 00:11:37 22335892 reads; of these: 22335892 (100.00%) were paired; of these: 618968 (2.77%) aligned concordantly 0 times 19603448 (87.77%) aligned concordantly exactly 1 time 2113476 (9.46%) aligned concordantly >1 times ---- 618968 pairs aligned concordantly 0 times; of these: 21696 (3.51%) aligned discordantly 1 time ---- 597272 pairs aligned 0 times concordantly or discordantly; of these: 1194544 mates make up the pairs; of these: 986029 (82.54%) aligned 0 times 177633 (14.87%) aligned exactly 1 time 30882 (2.59%) aligned >1 times 97.79% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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 20 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] 3238591 / 21722007 = 0.1491 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 10:41:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.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 10:41:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:41:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:04: 1000000 INFO @ Wed, 22 Apr 2020 10:42:09: 2000000 INFO @ Wed, 22 Apr 2020 10:42:14: 3000000 INFO @ Wed, 22 Apr 2020 10:42:20: 4000000 INFO @ Wed, 22 Apr 2020 10:42:26: 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 10:42:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.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 10:42:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:42:31: 6000000 INFO @ Wed, 22 Apr 2020 10:42:33: 1000000 INFO @ Wed, 22 Apr 2020 10:42:36: 7000000 INFO @ Wed, 22 Apr 2020 10:42:39: 2000000 INFO @ Wed, 22 Apr 2020 10:42:44: 8000000 INFO @ Wed, 22 Apr 2020 10:42:44: 3000000 INFO @ Wed, 22 Apr 2020 10:42:50: 4000000 INFO @ Wed, 22 Apr 2020 10:42:51: 9000000 INFO @ Wed, 22 Apr 2020 10:42:55: 5000000 INFO @ Wed, 22 Apr 2020 10:42:56: 10000000 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 10:42:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.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 10:42:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:42:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:43:01: 6000000 INFO @ Wed, 22 Apr 2020 10:43:02: 11000000 INFO @ Wed, 22 Apr 2020 10:43:04: 1000000 INFO @ Wed, 22 Apr 2020 10:43:06: 7000000 INFO @ Wed, 22 Apr 2020 10:43:08: 12000000 INFO @ Wed, 22 Apr 2020 10:43:09: 2000000 INFO @ Wed, 22 Apr 2020 10:43:12: 8000000 INFO @ Wed, 22 Apr 2020 10:43:14: 13000000 INFO @ Wed, 22 Apr 2020 10:43:15: 3000000 INFO @ Wed, 22 Apr 2020 10:43:17: 9000000 INFO @ Wed, 22 Apr 2020 10:43:20: 14000000 INFO @ Wed, 22 Apr 2020 10:43:20: 4000000 INFO @ Wed, 22 Apr 2020 10:43:23: 10000000 INFO @ Wed, 22 Apr 2020 10:43:26: 5000000 INFO @ Wed, 22 Apr 2020 10:43:26: 15000000 INFO @ Wed, 22 Apr 2020 10:43:29: 11000000 INFO @ Wed, 22 Apr 2020 10:43:31: 6000000 INFO @ Wed, 22 Apr 2020 10:43:32: 16000000 INFO @ Wed, 22 Apr 2020 10:43:34: 12000000 INFO @ Wed, 22 Apr 2020 10:43:37: 7000000 INFO @ Wed, 22 Apr 2020 10:43:38: 17000000 INFO @ Wed, 22 Apr 2020 10:43:40: 13000000 INFO @ Wed, 22 Apr 2020 10:43:42: 8000000 INFO @ Wed, 22 Apr 2020 10:43:44: 18000000 INFO @ Wed, 22 Apr 2020 10:43:45: 14000000 INFO @ Wed, 22 Apr 2020 10:43:48: 9000000 INFO @ Wed, 22 Apr 2020 10:43:50: 19000000 INFO @ Wed, 22 Apr 2020 10:43:51: 15000000 INFO @ Wed, 22 Apr 2020 10:43:54: 10000000 INFO @ Wed, 22 Apr 2020 10:43:56: 16000000 INFO @ Wed, 22 Apr 2020 10:43:57: 20000000 INFO @ Wed, 22 Apr 2020 10:43:59: 11000000 INFO @ Wed, 22 Apr 2020 10:44:02: 17000000 INFO @ Wed, 22 Apr 2020 10:44:03: 21000000 INFO @ Wed, 22 Apr 2020 10:44:04: 12000000 INFO @ Wed, 22 Apr 2020 10:44:07: 18000000 INFO @ Wed, 22 Apr 2020 10:44:09: 22000000 INFO @ Wed, 22 Apr 2020 10:44:09: 13000000 INFO @ Wed, 22 Apr 2020 10:44:12: 19000000 INFO @ Wed, 22 Apr 2020 10:44:15: 14000000 INFO @ Wed, 22 Apr 2020 10:44:15: 23000000 INFO @ Wed, 22 Apr 2020 10:44:17: 20000000 INFO @ Wed, 22 Apr 2020 10:44:20: 15000000 INFO @ Wed, 22 Apr 2020 10:44:21: 24000000 INFO @ Wed, 22 Apr 2020 10:44:23: 21000000 INFO @ Wed, 22 Apr 2020 10:44:25: 16000000 INFO @ Wed, 22 Apr 2020 10:44:27: 25000000 INFO @ Wed, 22 Apr 2020 10:44:28: 22000000 INFO @ Wed, 22 Apr 2020 10:44:30: 17000000 INFO @ Wed, 22 Apr 2020 10:44:33: 26000000 INFO @ Wed, 22 Apr 2020 10:44:34: 23000000 INFO @ Wed, 22 Apr 2020 10:44:35: 18000000 INFO @ Wed, 22 Apr 2020 10:44:39: 24000000 INFO @ Wed, 22 Apr 2020 10:44:39: 27000000 INFO @ Wed, 22 Apr 2020 10:44:41: 19000000 INFO @ Wed, 22 Apr 2020 10:44:44: 25000000 INFO @ Wed, 22 Apr 2020 10:44:45: 28000000 INFO @ Wed, 22 Apr 2020 10:44:46: 20000000 INFO @ Wed, 22 Apr 2020 10:44:49: 26000000 INFO @ Wed, 22 Apr 2020 10:44:51: 29000000 INFO @ Wed, 22 Apr 2020 10:44:51: 21000000 INFO @ Wed, 22 Apr 2020 10:44:55: 27000000 INFO @ Wed, 22 Apr 2020 10:44:56: 22000000 INFO @ Wed, 22 Apr 2020 10:44:57: 30000000 INFO @ Wed, 22 Apr 2020 10:45:00: 28000000 INFO @ Wed, 22 Apr 2020 10:45:01: 23000000 INFO @ Wed, 22 Apr 2020 10:45:02: 31000000 INFO @ Wed, 22 Apr 2020 10:45:05: 29000000 INFO @ Wed, 22 Apr 2020 10:45:07: 24000000 INFO @ Wed, 22 Apr 2020 10:45:08: 32000000 INFO @ Wed, 22 Apr 2020 10:45:10: 30000000 INFO @ Wed, 22 Apr 2020 10:45:12: 25000000 INFO @ Wed, 22 Apr 2020 10:45:14: 33000000 INFO @ Wed, 22 Apr 2020 10:45:15: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:45:17: 26000000 INFO @ Wed, 22 Apr 2020 10:45:20: 34000000 INFO @ Wed, 22 Apr 2020 10:45:20: 32000000 INFO @ Wed, 22 Apr 2020 10:45:22: 27000000 INFO @ Wed, 22 Apr 2020 10:45:26: 33000000 INFO @ Wed, 22 Apr 2020 10:45:26: 35000000 INFO @ Wed, 22 Apr 2020 10:45:27: 28000000 INFO @ Wed, 22 Apr 2020 10:45:31: 34000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:45:32: 36000000 INFO @ Wed, 22 Apr 2020 10:45:32: 29000000 INFO @ Wed, 22 Apr 2020 10:45:36: 35000000 INFO @ Wed, 22 Apr 2020 10:45:38: 30000000 INFO @ Wed, 22 Apr 2020 10:45:38: 37000000 INFO @ Wed, 22 Apr 2020 10:45:39: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:39: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:39: #1 total tags in treatment: 18479130 INFO @ Wed, 22 Apr 2020 10:45:39: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:39: #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 10:45:39: #1 tags after filtering in treatment: 10536747 INFO @ Wed, 22 Apr 2020 10:45:39: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:45:39: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:39: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:40: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:45:40: 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 10:45:40: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.05_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/SRX7409612/SRX7409612.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:41: 36000000 INFO @ Wed, 22 Apr 2020 10:45:43: 31000000 INFO @ Wed, 22 Apr 2020 10:45:46: 37000000 INFO @ Wed, 22 Apr 2020 10:45:47: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:45:47: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:45:47: #1 total tags in treatment: 18479130 INFO @ Wed, 22 Apr 2020 10:45:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:45:47: #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 10:45:48: 32000000 INFO @ Wed, 22 Apr 2020 10:45:48: #1 tags after filtering in treatment: 10536747 INFO @ Wed, 22 Apr 2020 10:45:48: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:45:48: #1 finished! INFO @ Wed, 22 Apr 2020 10:45:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:45:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:45:48: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:45:48: 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 10:45:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.10_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/SRX7409612/SRX7409612.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:45:52: 33000000 INFO @ Wed, 22 Apr 2020 10:45:57: 34000000 INFO @ Wed, 22 Apr 2020 10:46:02: 35000000 INFO @ Wed, 22 Apr 2020 10:46:07: 36000000 INFO @ Wed, 22 Apr 2020 10:46:11: 37000000 INFO @ Wed, 22 Apr 2020 10:46:13: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:46:13: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:46:13: #1 total tags in treatment: 18479130 INFO @ Wed, 22 Apr 2020 10:46:13: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:46:13: #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 10:46:13: #1 tags after filtering in treatment: 10536747 INFO @ Wed, 22 Apr 2020 10:46:13: #1 Redundant rate of treatment: 0.43 INFO @ Wed, 22 Apr 2020 10:46:13: #1 finished! INFO @ Wed, 22 Apr 2020 10:46:13: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:46:14: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:46:14: 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 10:46:14: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.20_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/SRX7409612/SRX7409612.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409612/SRX7409612.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling