Job ID = 5790992 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:07:15 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T23:07:15 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.198' 2020-04-21T23:07:15 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (165.112.9.235) from '172.19.7.198' 2020-04-21T23:07:15 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra2/SRR/008886/SRR9099528' 2020-04-21T23:07:15 fasterq-dump.2.9.6 err: invalid accession 'SRR9099528' spots read : 2,381,153 reads read : 4,762,306 reads written : 4,762,306 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: 00:01:35 2381153 reads; of these: 2381153 (100.00%) were paired; of these: 100504 (4.22%) aligned concordantly 0 times 2063182 (86.65%) aligned concordantly exactly 1 time 217467 (9.13%) aligned concordantly >1 times ---- 100504 pairs aligned concordantly 0 times; of these: 988 (0.98%) aligned discordantly 1 time ---- 99516 pairs aligned 0 times concordantly or discordantly; of these: 199032 mates make up the pairs; of these: 186794 (93.85%) aligned 0 times 9954 (5.00%) aligned exactly 1 time 2284 (1.15%) aligned >1 times 96.08% overall alignment rate Time searching: 00:01:35 Overall time: 00:01:35 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_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] 12371 / 2255082 = 0.0055 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 08:14:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.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 08:14:36: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:14:36: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:41: 1000000 INFO @ Wed, 22 Apr 2020 08:14:47: 2000000 INFO @ Wed, 22 Apr 2020 08:14:52: 3000000 INFO @ Wed, 22 Apr 2020 08:14:58: 4000000 INFO @ Wed, 22 Apr 2020 08:15:01: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 08:15:01: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 08:15:01: #1 total tags in treatment: 2268278 INFO @ Wed, 22 Apr 2020 08:15:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:01: #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 08:15:01: #1 tags after filtering in treatment: 2142829 INFO @ Wed, 22 Apr 2020 08:15:01: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 08:15:01: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:01: #2 number of paired peaks: 2 WARNING @ Wed, 22 Apr 2020 08:15:01: Too few paired peaks (2) 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 08:15:01: Process for pairing-model is terminated! 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 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.05_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/SRX5874491/SRX5874491.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:15:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.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 08:15:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:12: 1000000 INFO @ Wed, 22 Apr 2020 08:15:18: 2000000 INFO @ Wed, 22 Apr 2020 08:15:24: 3000000 INFO @ Wed, 22 Apr 2020 08:15:29: 4000000 INFO @ Wed, 22 Apr 2020 08:15:32: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 08:15:32: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 08:15:32: #1 total tags in treatment: 2268278 INFO @ Wed, 22 Apr 2020 08:15:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:32: #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 08:15:32: #1 tags after filtering in treatment: 2142829 INFO @ Wed, 22 Apr 2020 08:15:32: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 08:15:32: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:32: #2 number of paired peaks: 2 WARNING @ Wed, 22 Apr 2020 08:15:32: Too few paired peaks (2) 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 08:15:32: Process for pairing-model is terminated! 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 cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.10_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/SRX5874491/SRX5874491.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.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 08:15:37: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:37: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:42: 1000000 INFO @ Wed, 22 Apr 2020 08:15:48: 2000000 INFO @ Wed, 22 Apr 2020 08:15:53: 3000000 INFO @ Wed, 22 Apr 2020 08:15:59: 4000000 INFO @ Wed, 22 Apr 2020 08:16:01: #1 tag size is determined as 75 bps INFO @ Wed, 22 Apr 2020 08:16:01: #1 tag size = 75 INFO @ Wed, 22 Apr 2020 08:16:01: #1 total tags in treatment: 2268278 INFO @ Wed, 22 Apr 2020 08:16:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:01: #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 08:16:01: #1 tags after filtering in treatment: 2142829 INFO @ Wed, 22 Apr 2020 08:16:01: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 22 Apr 2020 08:16:01: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:02: #2 number of paired peaks: 2 WARNING @ Wed, 22 Apr 2020 08:16:02: Too few paired peaks (2) 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 08:16:02: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.20_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/SRX5874491/SRX5874491.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5874491/SRX5874491.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。