Job ID = 5791301 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:26:07 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 ) 2020-04-22T00:27:44 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( ) 2020-04-22T00:27:44 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 ) 2020-04-22T00:27:44 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 ) 2020-04-22T00:34:54 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 : 22,627,738 reads read : 45,255,476 reads written : 45,255,476 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: 00:12:27 22627738 reads; of these: 22627738 (100.00%) were paired; of these: 449039 (1.98%) aligned concordantly 0 times 19593867 (86.59%) aligned concordantly exactly 1 time 2584832 (11.42%) aligned concordantly >1 times ---- 449039 pairs aligned concordantly 0 times; of these: 37316 (8.31%) aligned discordantly 1 time ---- 411723 pairs aligned 0 times concordantly or discordantly; of these: 823446 mates make up the pairs; of these: 670364 (81.41%) aligned 0 times 117432 (14.26%) aligned exactly 1 time 35650 (4.33%) aligned >1 times 98.52% overall alignment rate Time searching: 00:12:27 Overall time: 00:12:27 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] 4046116 / 22186603 = 0.1824 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 10:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.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 10:01:10: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:01:10: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:01:17: 1000000 INFO @ Wed, 22 Apr 2020 10:01:23: 2000000 INFO @ Wed, 22 Apr 2020 10:01:29: 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 10:01:36: 4000000 INFO @ Wed, 22 Apr 2020 10:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.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 10:01:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:01:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:01:43: 5000000 INFO @ Wed, 22 Apr 2020 10:01:45: 1000000 INFO @ Wed, 22 Apr 2020 10:01:50: 6000000 INFO @ Wed, 22 Apr 2020 10:01:53: 2000000 INFO @ Wed, 22 Apr 2020 10:01:58: 7000000 INFO @ Wed, 22 Apr 2020 10:01:59: 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 10:02:05: 8000000 INFO @ Wed, 22 Apr 2020 10:02:06: 4000000 INFO @ Wed, 22 Apr 2020 10:02:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.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 10:02:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:02:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:02:12: 9000000 INFO @ Wed, 22 Apr 2020 10:02:14: 5000000 INFO @ Wed, 22 Apr 2020 10:02:14: 1000000 INFO @ Wed, 22 Apr 2020 10:02:20: 10000000 INFO @ Wed, 22 Apr 2020 10:02:21: 6000000 INFO @ Wed, 22 Apr 2020 10:02:21: 2000000 INFO @ Wed, 22 Apr 2020 10:02:27: 11000000 INFO @ Wed, 22 Apr 2020 10:02:28: 7000000 INFO @ Wed, 22 Apr 2020 10:02:29: 3000000 INFO @ Wed, 22 Apr 2020 10:02:34: 12000000 INFO @ Wed, 22 Apr 2020 10:02:35: 8000000 INFO @ Wed, 22 Apr 2020 10:02:36: 4000000 INFO @ Wed, 22 Apr 2020 10:02:42: 13000000 INFO @ Wed, 22 Apr 2020 10:02:42: 9000000 INFO @ Wed, 22 Apr 2020 10:02:43: 5000000 INFO @ Wed, 22 Apr 2020 10:02:49: 14000000 INFO @ Wed, 22 Apr 2020 10:02:50: 10000000 INFO @ Wed, 22 Apr 2020 10:02:53: 6000000 INFO @ Wed, 22 Apr 2020 10:02:56: 15000000 INFO @ Wed, 22 Apr 2020 10:02:58: 11000000 INFO @ Wed, 22 Apr 2020 10:03:03: 16000000 INFO @ Wed, 22 Apr 2020 10:03:04: 7000000 INFO @ Wed, 22 Apr 2020 10:03:05: 12000000 INFO @ Wed, 22 Apr 2020 10:03:11: 17000000 INFO @ Wed, 22 Apr 2020 10:03:13: 13000000 INFO @ Wed, 22 Apr 2020 10:03:14: 8000000 INFO @ Wed, 22 Apr 2020 10:03:18: 18000000 INFO @ Wed, 22 Apr 2020 10:03:20: 14000000 INFO @ Wed, 22 Apr 2020 10:03:25: 19000000 INFO @ Wed, 22 Apr 2020 10:03:25: 9000000 INFO @ Wed, 22 Apr 2020 10:03:28: 15000000 INFO @ Wed, 22 Apr 2020 10:03:32: 20000000 INFO @ Wed, 22 Apr 2020 10:03:36: 16000000 INFO @ Wed, 22 Apr 2020 10:03:37: 10000000 INFO @ Wed, 22 Apr 2020 10:03:40: 21000000 INFO @ Wed, 22 Apr 2020 10:03:44: 17000000 INFO @ Wed, 22 Apr 2020 10:03:47: 22000000 INFO @ Wed, 22 Apr 2020 10:03:47: 11000000 INFO @ Wed, 22 Apr 2020 10:03:51: 18000000 INFO @ Wed, 22 Apr 2020 10:03:54: 23000000 INFO @ Wed, 22 Apr 2020 10:03:55: 12000000 INFO @ Wed, 22 Apr 2020 10:03:59: 19000000 INFO @ Wed, 22 Apr 2020 10:04:02: 24000000 INFO @ Wed, 22 Apr 2020 10:04:02: 13000000 INFO @ Wed, 22 Apr 2020 10:04:07: 20000000 INFO @ Wed, 22 Apr 2020 10:04:09: 25000000 INFO @ Wed, 22 Apr 2020 10:04:09: 14000000 INFO @ Wed, 22 Apr 2020 10:04:16: 26000000 INFO @ Wed, 22 Apr 2020 10:04:16: 15000000 INFO @ Wed, 22 Apr 2020 10:04:22: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:04:23: 27000000 INFO @ Wed, 22 Apr 2020 10:04:23: 16000000 INFO @ Wed, 22 Apr 2020 10:04:30: 28000000 INFO @ Wed, 22 Apr 2020 10:04:30: 17000000 INFO @ Wed, 22 Apr 2020 10:04:37: 29000000 INFO @ Wed, 22 Apr 2020 10:04:37: 18000000 INFO @ Wed, 22 Apr 2020 10:04:38: 22000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:04:44: 30000000 INFO @ Wed, 22 Apr 2020 10:04:44: 19000000 INFO @ Wed, 22 Apr 2020 10:04:46: 23000000 INFO @ Wed, 22 Apr 2020 10:04:51: 31000000 INFO @ Wed, 22 Apr 2020 10:04:51: 20000000 INFO @ Wed, 22 Apr 2020 10:04:54: 24000000 INFO @ Wed, 22 Apr 2020 10:04:58: 32000000 INFO @ Wed, 22 Apr 2020 10:04:58: 21000000 INFO @ Wed, 22 Apr 2020 10:05:01: 25000000 INFO @ Wed, 22 Apr 2020 10:05:05: 33000000 INFO @ Wed, 22 Apr 2020 10:05:05: 22000000 INFO @ Wed, 22 Apr 2020 10:05:08: 26000000 INFO @ Wed, 22 Apr 2020 10:05:12: 34000000 INFO @ Wed, 22 Apr 2020 10:05:13: 23000000 INFO @ Wed, 22 Apr 2020 10:05:15: 27000000 INFO @ Wed, 22 Apr 2020 10:05:19: 35000000 INFO @ Wed, 22 Apr 2020 10:05:20: 24000000 INFO @ Wed, 22 Apr 2020 10:05:22: 28000000 INFO @ Wed, 22 Apr 2020 10:05:26: 36000000 INFO @ Wed, 22 Apr 2020 10:05:27: 25000000 INFO @ Wed, 22 Apr 2020 10:05:29: 29000000 INFO @ Wed, 22 Apr 2020 10:05:29: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:05:29: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:05:29: #1 total tags in treatment: 18133557 INFO @ Wed, 22 Apr 2020 10:05:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:05:29: #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 10:05:29: #1 tags after filtering in treatment: 11802983 INFO @ Wed, 22 Apr 2020 10:05:29: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 10:05:29: #1 finished! INFO @ Wed, 22 Apr 2020 10:05:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:05:30: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:05:30: 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 10:05:30: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:05:33: 26000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.05_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/SRX7409558/SRX7409558.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:05:35: 30000000 INFO @ Wed, 22 Apr 2020 10:05:40: 27000000 INFO @ Wed, 22 Apr 2020 10:05:42: 31000000 INFO @ Wed, 22 Apr 2020 10:05:47: 28000000 INFO @ Wed, 22 Apr 2020 10:05:48: 32000000 INFO @ Wed, 22 Apr 2020 10:05:53: 29000000 INFO @ Wed, 22 Apr 2020 10:05:55: 33000000 INFO @ Wed, 22 Apr 2020 10:06:00: 30000000 INFO @ Wed, 22 Apr 2020 10:06:01: 34000000 INFO @ Wed, 22 Apr 2020 10:06:06: 31000000 INFO @ Wed, 22 Apr 2020 10:06:08: 35000000 INFO @ Wed, 22 Apr 2020 10:06:13: 32000000 INFO @ Wed, 22 Apr 2020 10:06:15: 36000000 INFO @ Wed, 22 Apr 2020 10:06:18: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:06:18: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:06:18: #1 total tags in treatment: 18133557 INFO @ Wed, 22 Apr 2020 10:06:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:06:18: #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 10:06:18: #1 tags after filtering in treatment: 11802983 INFO @ Wed, 22 Apr 2020 10:06:18: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 10:06:18: #1 finished! INFO @ Wed, 22 Apr 2020 10:06:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:06:19: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:06:19: 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 10:06:19: Process for pairing-model is terminated! INFO @ Wed, 22 Apr 2020 10:06:20: 33000000 cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.10_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/SRX7409558/SRX7409558.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:06:26: 34000000 INFO @ Wed, 22 Apr 2020 10:06:32: 35000000 INFO @ Wed, 22 Apr 2020 10:06:39: 36000000 INFO @ Wed, 22 Apr 2020 10:06:42: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:06:42: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:06:42: #1 total tags in treatment: 18133557 INFO @ Wed, 22 Apr 2020 10:06:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:06:42: #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 10:06:42: #1 tags after filtering in treatment: 11802983 INFO @ Wed, 22 Apr 2020 10:06:42: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 10:06:42: #1 finished! INFO @ Wed, 22 Apr 2020 10:06:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:06:43: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:06:43: 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 10:06:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.20_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/SRX7409558/SRX7409558.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409558/SRX7409558.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling