Job ID = 5720730 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:02:29 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 ) 2020-04-15T16:02:29 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.231' from '172.19.7.191' 2020-04-15T16:02:29 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' (165.112.9.231) from '172.19.7.191' 2020-04-15T16:02:29 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/sra70/SRR/007616/SRR7799020' 2020-04-15T16:02:29 fasterq-dump.2.9.6 err: cmn_iter.c cmn_iter_open_db().VDBManagerOpenDBRead( 'SRR7799020' ) -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-15T16:02:29 fasterq-dump.2.9.6 err: make_fastq_iter() -> RC(rcKrypto,rcFile,rcOpening,rcConnection,rcFailed) 2020-04-15T16:03:05 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 ) 2020-04-15T16:03:05 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 ) 2020-04-15T16:06:33 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 ) 2020-04-15T16:06:33 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 ) 2020-04-15T16:06:33 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 ) 2020-04-15T16:14:37 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 ) 2020-04-15T16:14:37 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 : 32,838,994 reads read : 65,677,988 reads written : 65,677,988 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: 00:06:28 32838994 reads; of these: 32838994 (100.00%) were paired; of these: 31599921 (96.23%) aligned concordantly 0 times 1015586 (3.09%) aligned concordantly exactly 1 time 223487 (0.68%) aligned concordantly >1 times ---- 31599921 pairs aligned concordantly 0 times; of these: 7815 (0.02%) aligned discordantly 1 time ---- 31592106 pairs aligned 0 times concordantly or discordantly; of these: 63184212 mates make up the pairs; of these: 62262837 (98.54%) aligned 0 times 466696 (0.74%) aligned exactly 1 time 454679 (0.72%) aligned >1 times 5.20% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 40813 / 1240654 = 0.0329 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 @ Thu, 16 Apr 2020 01:45:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:45:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:45:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:45:30: 1000000 INFO @ Thu, 16 Apr 2020 01:45:34: 2000000 INFO @ Thu, 16 Apr 2020 01:45:38: 3000000 INFO @ Thu, 16 Apr 2020 01:45:39: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 01:45:39: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 01:45:39: #1 total tags in treatment: 1198314 INFO @ Thu, 16 Apr 2020 01:45:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:45:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:45:39: #1 tags after filtering in treatment: 1165800 INFO @ Thu, 16 Apr 2020 01:45:39: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 01:45:39: #1 finished! INFO @ Thu, 16 Apr 2020 01:45:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:45:40: #2 number of paired peaks: 1198 INFO @ Thu, 16 Apr 2020 01:45:40: start model_add_line... INFO @ Thu, 16 Apr 2020 01:45:40: start X-correlation... INFO @ Thu, 16 Apr 2020 01:45:40: end of X-cor INFO @ Thu, 16 Apr 2020 01:45:40: #2 finished! INFO @ Thu, 16 Apr 2020 01:45:40: #2 predicted fragment length is 138 bps INFO @ Thu, 16 Apr 2020 01:45:40: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 16 Apr 2020 01:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.05_model.r INFO @ Thu, 16 Apr 2020 01:45:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:45:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.05_summits.bed INFO @ Thu, 16 Apr 2020 01:45:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:45:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:45:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:45:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:46:00: 1000000 INFO @ Thu, 16 Apr 2020 01:46:04: 2000000 INFO @ Thu, 16 Apr 2020 01:46:08: 3000000 INFO @ Thu, 16 Apr 2020 01:46:09: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 01:46:09: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 01:46:09: #1 total tags in treatment: 1198314 INFO @ Thu, 16 Apr 2020 01:46:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:46:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:46:09: #1 tags after filtering in treatment: 1165800 INFO @ Thu, 16 Apr 2020 01:46:09: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 01:46:09: #1 finished! INFO @ Thu, 16 Apr 2020 01:46:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:46:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:46:10: #2 number of paired peaks: 1198 INFO @ Thu, 16 Apr 2020 01:46:10: start model_add_line... INFO @ Thu, 16 Apr 2020 01:46:10: start X-correlation... INFO @ Thu, 16 Apr 2020 01:46:10: end of X-cor INFO @ Thu, 16 Apr 2020 01:46:10: #2 finished! INFO @ Thu, 16 Apr 2020 01:46:10: #2 predicted fragment length is 138 bps INFO @ Thu, 16 Apr 2020 01:46:10: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 16 Apr 2020 01:46:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.10_model.r INFO @ Thu, 16 Apr 2020 01:46:10: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:46:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:46:12: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:46:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:46:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:46:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.10_summits.bed INFO @ Thu, 16 Apr 2020 01:46:14: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:46:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:46:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:46:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:46:30: 1000000 INFO @ Thu, 16 Apr 2020 01:46:34: 2000000 INFO @ Thu, 16 Apr 2020 01:46:38: 3000000 INFO @ Thu, 16 Apr 2020 01:46:39: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 01:46:39: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 01:46:39: #1 total tags in treatment: 1198314 INFO @ Thu, 16 Apr 2020 01:46:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:46:39: #1 tags after filtering in treatment: 1165800 INFO @ Thu, 16 Apr 2020 01:46:39: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 01:46:39: #1 finished! INFO @ Thu, 16 Apr 2020 01:46:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:46:40: #2 number of paired peaks: 1198 INFO @ Thu, 16 Apr 2020 01:46:40: start model_add_line... INFO @ Thu, 16 Apr 2020 01:46:40: start X-correlation... INFO @ Thu, 16 Apr 2020 01:46:40: end of X-cor INFO @ Thu, 16 Apr 2020 01:46:40: #2 finished! INFO @ Thu, 16 Apr 2020 01:46:40: #2 predicted fragment length is 138 bps INFO @ Thu, 16 Apr 2020 01:46:40: #2 alternative fragment length(s) may be 138 bps INFO @ Thu, 16 Apr 2020 01:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.20_model.r INFO @ Thu, 16 Apr 2020 01:46:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:46:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4650861/SRX4650861.20_summits.bed INFO @ Thu, 16 Apr 2020 01:46:44: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (42 records, 4 fields): 0 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。