Job ID = 5791286 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:23:01 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 ) 2020-04-22T00:36:15 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 ) 2020-04-22T00:36:15 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 ) 2020-04-22T00:36:15 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 ) 2020-04-22T00:36:15 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 : 32,564,814 reads read : 65,129,628 reads written : 65,129,628 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: 00:18:26 32564814 reads; of these: 32564814 (100.00%) were paired; of these: 1791198 (5.50%) aligned concordantly 0 times 27355530 (84.00%) aligned concordantly exactly 1 time 3418086 (10.50%) aligned concordantly >1 times ---- 1791198 pairs aligned concordantly 0 times; of these: 42184 (2.36%) aligned discordantly 1 time ---- 1749014 pairs aligned 0 times concordantly or discordantly; of these: 3498028 mates make up the pairs; of these: 3111160 (88.94%) aligned 0 times 327408 (9.36%) aligned exactly 1 time 59460 (1.70%) aligned >1 times 95.22% overall alignment rate Time searching: 00:18:26 Overall time: 00:18:26 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 28 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] 10077933 / 30781486 = 0.3274 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 10:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.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 10:10:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:10:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:10:44: 1000000 INFO @ Wed, 22 Apr 2020 10:10:49: 2000000 INFO @ Wed, 22 Apr 2020 10:10:54: 3000000 INFO @ Wed, 22 Apr 2020 10:10:58: 4000000 INFO @ Wed, 22 Apr 2020 10:11:03: 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 10:11:08: 6000000 INFO @ Wed, 22 Apr 2020 10:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.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 10:11:09: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:11:09: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:11:13: 7000000 INFO @ Wed, 22 Apr 2020 10:11:14: 1000000 INFO @ Wed, 22 Apr 2020 10:11:18: 8000000 INFO @ Wed, 22 Apr 2020 10:11:20: 2000000 INFO @ Wed, 22 Apr 2020 10:11:23: 9000000 INFO @ Wed, 22 Apr 2020 10:11:26: 3000000 INFO @ Wed, 22 Apr 2020 10:11:29: 10000000 INFO @ Wed, 22 Apr 2020 10:11:31: 4000000 INFO @ Wed, 22 Apr 2020 10:11:34: 11000000 INFO @ Wed, 22 Apr 2020 10:11:37: 5000000 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 10:11:39: 12000000 INFO @ Wed, 22 Apr 2020 10:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.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 10:11:39: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:11:39: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:11:43: 6000000 INFO @ Wed, 22 Apr 2020 10:11:44: 13000000 INFO @ Wed, 22 Apr 2020 10:11:45: 1000000 INFO @ Wed, 22 Apr 2020 10:11:48: 7000000 INFO @ Wed, 22 Apr 2020 10:11:49: 14000000 INFO @ Wed, 22 Apr 2020 10:11:50: 2000000 INFO @ Wed, 22 Apr 2020 10:11:53: 8000000 INFO @ Wed, 22 Apr 2020 10:11:54: 15000000 INFO @ Wed, 22 Apr 2020 10:11:56: 3000000 INFO @ Wed, 22 Apr 2020 10:11:59: 9000000 INFO @ Wed, 22 Apr 2020 10:11:59: 16000000 INFO @ Wed, 22 Apr 2020 10:12:01: 4000000 INFO @ Wed, 22 Apr 2020 10:12:04: 10000000 INFO @ Wed, 22 Apr 2020 10:12:04: 17000000 INFO @ Wed, 22 Apr 2020 10:12:07: 5000000 INFO @ Wed, 22 Apr 2020 10:12:09: 11000000 INFO @ Wed, 22 Apr 2020 10:12:09: 18000000 INFO @ Wed, 22 Apr 2020 10:12:12: 6000000 INFO @ Wed, 22 Apr 2020 10:12:14: 12000000 INFO @ Wed, 22 Apr 2020 10:12:14: 19000000 INFO @ Wed, 22 Apr 2020 10:12:17: 7000000 INFO @ Wed, 22 Apr 2020 10:12:19: 13000000 INFO @ Wed, 22 Apr 2020 10:12:19: 20000000 INFO @ Wed, 22 Apr 2020 10:12:23: 8000000 INFO @ Wed, 22 Apr 2020 10:12:24: 14000000 INFO @ Wed, 22 Apr 2020 10:12:24: 21000000 INFO @ Wed, 22 Apr 2020 10:12:28: 9000000 INFO @ Wed, 22 Apr 2020 10:12:29: 15000000 INFO @ Wed, 22 Apr 2020 10:12:29: 22000000 INFO @ Wed, 22 Apr 2020 10:12:33: 10000000 INFO @ Wed, 22 Apr 2020 10:12:34: 16000000 INFO @ Wed, 22 Apr 2020 10:12:35: 23000000 INFO @ Wed, 22 Apr 2020 10:12:38: 11000000 INFO @ Wed, 22 Apr 2020 10:12:39: 17000000 INFO @ Wed, 22 Apr 2020 10:12:40: 24000000 INFO @ Wed, 22 Apr 2020 10:12:44: 12000000 INFO @ Wed, 22 Apr 2020 10:12:45: 18000000 INFO @ Wed, 22 Apr 2020 10:12:45: 25000000 INFO @ Wed, 22 Apr 2020 10:12:49: 13000000 INFO @ Wed, 22 Apr 2020 10:12:51: 26000000 INFO @ Wed, 22 Apr 2020 10:12:51: 19000000 INFO @ Wed, 22 Apr 2020 10:12:54: 14000000 INFO @ Wed, 22 Apr 2020 10:12:56: 27000000 INFO @ Wed, 22 Apr 2020 10:12:57: 20000000 INFO @ Wed, 22 Apr 2020 10:12:59: 15000000 INFO @ Wed, 22 Apr 2020 10:13:01: 28000000 INFO @ Wed, 22 Apr 2020 10:13:02: 21000000 INFO @ Wed, 22 Apr 2020 10:13:04: 16000000 INFO @ Wed, 22 Apr 2020 10:13:07: 29000000 INFO @ Wed, 22 Apr 2020 10:13:07: 22000000 INFO @ Wed, 22 Apr 2020 10:13:09: 17000000 INFO @ Wed, 22 Apr 2020 10:13:12: 30000000 INFO @ Wed, 22 Apr 2020 10:13:12: 23000000 INFO @ Wed, 22 Apr 2020 10:13:15: 18000000 INFO @ Wed, 22 Apr 2020 10:13:17: 24000000 INFO @ Wed, 22 Apr 2020 10:13:17: 31000000 INFO @ Wed, 22 Apr 2020 10:13:20: 19000000 INFO @ Wed, 22 Apr 2020 10:13:23: 32000000 INFO @ Wed, 22 Apr 2020 10:13:23: 25000000 INFO @ Wed, 22 Apr 2020 10:13:25: 20000000 INFO @ Wed, 22 Apr 2020 10:13:28: 33000000 INFO @ Wed, 22 Apr 2020 10:13:29: 26000000 INFO @ Wed, 22 Apr 2020 10:13:30: 21000000 INFO @ Wed, 22 Apr 2020 10:13:34: 34000000 INFO @ Wed, 22 Apr 2020 10:13:35: 27000000 INFO @ Wed, 22 Apr 2020 10:13:35: 22000000 INFO @ Wed, 22 Apr 2020 10:13:39: 35000000 INFO @ Wed, 22 Apr 2020 10:13:40: 23000000 INFO @ Wed, 22 Apr 2020 10:13:41: 28000000 INFO @ Wed, 22 Apr 2020 10:13:44: 36000000 INFO @ Wed, 22 Apr 2020 10:13:46: 24000000 INFO @ Wed, 22 Apr 2020 10:13:47: 29000000 INFO @ Wed, 22 Apr 2020 10:13:50: 37000000 INFO @ Wed, 22 Apr 2020 10:13:51: 25000000 INFO @ Wed, 22 Apr 2020 10:13:53: 30000000 INFO @ Wed, 22 Apr 2020 10:13:55: 38000000 INFO @ Wed, 22 Apr 2020 10:13:56: 26000000 INFO @ Wed, 22 Apr 2020 10:13:59: 31000000 INFO @ Wed, 22 Apr 2020 10:14:01: 39000000 INFO @ Wed, 22 Apr 2020 10:14:01: 27000000 INFO @ Wed, 22 Apr 2020 10:14:05: 32000000 INFO @ Wed, 22 Apr 2020 10:14:07: 40000000 INFO @ Wed, 22 Apr 2020 10:14:07: 28000000 INFO @ Wed, 22 Apr 2020 10:14:10: 33000000 INFO @ Wed, 22 Apr 2020 10:14:12: 41000000 INFO @ Wed, 22 Apr 2020 10:14:12: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 10:14:15: 34000000 INFO @ Wed, 22 Apr 2020 10:14:17: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:14:17: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:14:17: #1 total tags in treatment: 20698277 INFO @ Wed, 22 Apr 2020 10:14:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:14:17: #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 10:14:17: #1 tags after filtering in treatment: 12751482 INFO @ Wed, 22 Apr 2020 10:14:17: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 10:14:17: #1 finished! INFO @ Wed, 22 Apr 2020 10:14:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:14:17: 30000000 INFO @ Wed, 22 Apr 2020 10:14:18: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:14:18: 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 10:14:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.05_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/SRX7409545/SRX7409545.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:14:20: 35000000 INFO @ Wed, 22 Apr 2020 10:14:23: 31000000 INFO @ Wed, 22 Apr 2020 10:14:26: 36000000 INFO @ Wed, 22 Apr 2020 10:14:28: 32000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 10:14:31: 37000000 INFO @ Wed, 22 Apr 2020 10:14:33: 33000000 INFO @ Wed, 22 Apr 2020 10:14:36: 38000000 INFO @ Wed, 22 Apr 2020 10:14:38: 34000000 INFO @ Wed, 22 Apr 2020 10:14:41: 39000000 INFO @ Wed, 22 Apr 2020 10:14:43: 35000000 INFO @ Wed, 22 Apr 2020 10:14:46: 40000000 INFO @ Wed, 22 Apr 2020 10:14:48: 36000000 INFO @ Wed, 22 Apr 2020 10:14:52: 41000000 INFO @ Wed, 22 Apr 2020 10:14:53: 37000000 INFO @ Wed, 22 Apr 2020 10:14:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:14:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:14:57: #1 total tags in treatment: 20698277 INFO @ Wed, 22 Apr 2020 10:14:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:14:57: #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 10:14:57: #1 tags after filtering in treatment: 12751482 INFO @ Wed, 22 Apr 2020 10:14:57: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 10:14:57: #1 finished! INFO @ Wed, 22 Apr 2020 10:14:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:14:58: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:14:58: 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 10:14:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.10_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/SRX7409545/SRX7409545.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:14:59: 38000000 INFO @ Wed, 22 Apr 2020 10:15:04: 39000000 INFO @ Wed, 22 Apr 2020 10:15:09: 40000000 INFO @ Wed, 22 Apr 2020 10:15:13: 41000000 INFO @ Wed, 22 Apr 2020 10:15:18: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 10:15:18: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 10:15:18: #1 total tags in treatment: 20698277 INFO @ Wed, 22 Apr 2020 10:15:18: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:15:18: #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 10:15:18: #1 tags after filtering in treatment: 12751482 INFO @ Wed, 22 Apr 2020 10:15:18: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 10:15:18: #1 finished! INFO @ Wed, 22 Apr 2020 10:15:18: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:15:19: #2 number of paired peaks: 0 WARNING @ Wed, 22 Apr 2020 10:15:19: 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 10:15:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.20_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/SRX7409545/SRX7409545.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX7409545/SRX7409545.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling