Job ID = 5790993 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 '172.19.7.192' 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 '172.19.7.192' 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/sra19/SRR/008886/SRR9099529' 2020-04-21T23:07:15 fasterq-dump.2.9.6 err: invalid accession 'SRR9099529' spots read : 5,158,221 reads read : 10,316,442 reads written : 10,316,442 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: 00:02:33 5158221 reads; of these: 5158221 (100.00%) were paired; of these: 662772 (12.85%) aligned concordantly 0 times 3439414 (66.68%) aligned concordantly exactly 1 time 1056035 (20.47%) aligned concordantly >1 times ---- 662772 pairs aligned concordantly 0 times; of these: 2517 (0.38%) aligned discordantly 1 time ---- 660255 pairs aligned 0 times concordantly or discordantly; of these: 1320510 mates make up the pairs; of these: 1276975 (96.70%) aligned 0 times 26935 (2.04%) aligned exactly 1 time 16600 (1.26%) aligned >1 times 87.62% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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] 308465 / 4496168 = 0.0686 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 08:16:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.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 08:16:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:21: 1000000 INFO @ Wed, 22 Apr 2020 08:16:25: 2000000 INFO @ Wed, 22 Apr 2020 08:16:29: 3000000 INFO @ Wed, 22 Apr 2020 08:16:33: 4000000 INFO @ Wed, 22 Apr 2020 08:16:36: 5000000 INFO @ Wed, 22 Apr 2020 08:16:40: 6000000 INFO @ Wed, 22 Apr 2020 08:16:44: 7000000 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 08:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.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 08:16:47: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:47: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:48: 8000000 INFO @ Wed, 22 Apr 2020 08:16:49: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:16:49: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:16:49: #1 total tags in treatment: 4187025 INFO @ Wed, 22 Apr 2020 08:16:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:49: #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 08:16:49: #1 tags after filtering in treatment: 3303227 INFO @ Wed, 22 Apr 2020 08:16:49: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:16:49: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:49: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:50: #2 number of paired peaks: 163 WARNING @ Wed, 22 Apr 2020 08:16:50: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:50: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:50: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:50: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:50: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:50: #2 predicted fragment length is 120 bps INFO @ Wed, 22 Apr 2020 08:16:50: #2 alternative fragment length(s) may be 1,100,120,160,182,562 bps INFO @ Wed, 22 Apr 2020 08:16:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.05_model.r INFO @ Wed, 22 Apr 2020 08:16:50: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:51: 1000000 INFO @ Wed, 22 Apr 2020 08:16:55: 2000000 INFO @ Wed, 22 Apr 2020 08:16:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:59: 3000000 INFO @ Wed, 22 Apr 2020 08:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.05_summits.bed INFO @ Wed, 22 Apr 2020 08:16:59: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (672 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:17:03: 4000000 INFO @ Wed, 22 Apr 2020 08:17:06: 5000000 INFO @ Wed, 22 Apr 2020 08:17:10: 6000000 INFO @ Wed, 22 Apr 2020 08:17:14: 7000000 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 08:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.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 08:17:17: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:17:17: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:18: 8000000 INFO @ Wed, 22 Apr 2020 08:17:20: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:17:20: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:17:20: #1 total tags in treatment: 4187025 INFO @ Wed, 22 Apr 2020 08:17:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:20: #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 08:17:20: #1 tags after filtering in treatment: 3303227 INFO @ Wed, 22 Apr 2020 08:17:20: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:17:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:20: #2 number of paired peaks: 163 WARNING @ Wed, 22 Apr 2020 08:17:20: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:20: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:20: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:20: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:20: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:20: #2 predicted fragment length is 120 bps INFO @ Wed, 22 Apr 2020 08:17:20: #2 alternative fragment length(s) may be 1,100,120,160,182,562 bps INFO @ Wed, 22 Apr 2020 08:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.10_model.r INFO @ Wed, 22 Apr 2020 08:17:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:17:22: 1000000 INFO @ Wed, 22 Apr 2020 08:17:26: 2000000 INFO @ Wed, 22 Apr 2020 08:17:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.10_summits.bed INFO @ Wed, 22 Apr 2020 08:17:30: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (437 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:17:30: 3000000 INFO @ Wed, 22 Apr 2020 08:17:35: 4000000 INFO @ Wed, 22 Apr 2020 08:17:40: 5000000 INFO @ Wed, 22 Apr 2020 08:17:44: 6000000 INFO @ Wed, 22 Apr 2020 08:17:49: 7000000 INFO @ Wed, 22 Apr 2020 08:17:53: 8000000 INFO @ Wed, 22 Apr 2020 08:17:55: #1 tag size is determined as 42 bps INFO @ Wed, 22 Apr 2020 08:17:55: #1 tag size = 42 INFO @ Wed, 22 Apr 2020 08:17:55: #1 total tags in treatment: 4187025 INFO @ Wed, 22 Apr 2020 08:17:55: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:55: #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 08:17:55: #1 tags after filtering in treatment: 3303227 INFO @ Wed, 22 Apr 2020 08:17:55: #1 Redundant rate of treatment: 0.21 INFO @ Wed, 22 Apr 2020 08:17:55: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:55: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:56: #2 number of paired peaks: 163 WARNING @ Wed, 22 Apr 2020 08:17:56: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:56: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:56: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:56: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:56: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:56: #2 predicted fragment length is 120 bps INFO @ Wed, 22 Apr 2020 08:17:56: #2 alternative fragment length(s) may be 1,100,120,160,182,562 bps INFO @ Wed, 22 Apr 2020 08:17:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.20_model.r INFO @ Wed, 22 Apr 2020 08:17:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:18:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:18:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:18:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:18:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874492/SRX5874492.20_summits.bed INFO @ Wed, 22 Apr 2020 08:18:06: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。