Job ID = 5790779 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:02:48 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 ) 2020-04-21T22:02:48 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.231' from '172.19.7.205' 2020-04-21T22:02:48 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 '172.19.7.205' 2020-04-21T22:02:48 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/sra47/SRR/010702/SRR10959054' 2020-04-21T22:02:48 fasterq-dump.2.9.6 err: invalid accession 'SRR10959054' 2020-04-21T22:12:38 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 ) 2020-04-21T22:12:38 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 : 21,180,185 reads read : 42,360,370 reads written : 21,180,185 reads 0-length : 21,180,185 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:51 21180185 reads; of these: 21180185 (100.00%) were unpaired; of these: 615040 (2.90%) aligned 0 times 15247285 (71.99%) aligned exactly 1 time 5317860 (25.11%) aligned >1 times 97.10% overall alignment rate Time searching: 00:13:52 Overall time: 00:13:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4028478 / 20565145 = 0.1959 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 07:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:34:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:34:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:34:20: 1000000 INFO @ Wed, 22 Apr 2020 07:34:25: 2000000 INFO @ Wed, 22 Apr 2020 07:34:30: 3000000 INFO @ Wed, 22 Apr 2020 07:34:36: 4000000 INFO @ Wed, 22 Apr 2020 07:34:41: 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 07:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:34:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:34:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:34:46: 6000000 INFO @ Wed, 22 Apr 2020 07:34:49: 1000000 INFO @ Wed, 22 Apr 2020 07:34:52: 7000000 INFO @ Wed, 22 Apr 2020 07:34:54: 2000000 INFO @ Wed, 22 Apr 2020 07:34:57: 8000000 INFO @ Wed, 22 Apr 2020 07:35:00: 3000000 INFO @ Wed, 22 Apr 2020 07:35:03: 9000000 INFO @ Wed, 22 Apr 2020 07:35:05: 4000000 INFO @ Wed, 22 Apr 2020 07:35:08: 10000000 INFO @ Wed, 22 Apr 2020 07:35:10: 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 07:35:13: 11000000 INFO @ Wed, 22 Apr 2020 07:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:35:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:35:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:35:15: 6000000 INFO @ Wed, 22 Apr 2020 07:35:19: 12000000 INFO @ Wed, 22 Apr 2020 07:35:19: 1000000 INFO @ Wed, 22 Apr 2020 07:35:21: 7000000 INFO @ Wed, 22 Apr 2020 07:35:25: 13000000 INFO @ Wed, 22 Apr 2020 07:35:25: 2000000 INFO @ Wed, 22 Apr 2020 07:35:26: 8000000 INFO @ Wed, 22 Apr 2020 07:35:30: 14000000 INFO @ Wed, 22 Apr 2020 07:35:30: 3000000 INFO @ Wed, 22 Apr 2020 07:35:31: 9000000 INFO @ Wed, 22 Apr 2020 07:35:35: 15000000 INFO @ Wed, 22 Apr 2020 07:35:35: 4000000 INFO @ Wed, 22 Apr 2020 07:35:36: 10000000 INFO @ Wed, 22 Apr 2020 07:35:41: 16000000 INFO @ Wed, 22 Apr 2020 07:35:41: 5000000 INFO @ Wed, 22 Apr 2020 07:35:42: 11000000 INFO @ Wed, 22 Apr 2020 07:35:44: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:35:44: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:35:44: #1 total tags in treatment: 16536667 INFO @ Wed, 22 Apr 2020 07:35:44: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:35:44: #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 07:35:44: #1 tags after filtering in treatment: 16536495 INFO @ Wed, 22 Apr 2020 07:35:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:35:44: #1 finished! INFO @ Wed, 22 Apr 2020 07:35:44: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:35:46: #2 number of paired peaks: 3577 INFO @ Wed, 22 Apr 2020 07:35:46: start model_add_line... INFO @ Wed, 22 Apr 2020 07:35:46: start X-correlation... INFO @ Wed, 22 Apr 2020 07:35:46: end of X-cor INFO @ Wed, 22 Apr 2020 07:35:46: #2 finished! INFO @ Wed, 22 Apr 2020 07:35:46: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 07:35:46: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 07:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.05_model.r WARNING @ Wed, 22 Apr 2020 07:35:46: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:35:46: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 22 Apr 2020 07:35:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:35:46: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:35:46: 6000000 INFO @ Wed, 22 Apr 2020 07:35:47: 12000000 INFO @ Wed, 22 Apr 2020 07:35:51: 7000000 INFO @ Wed, 22 Apr 2020 07:35:52: 13000000 INFO @ Wed, 22 Apr 2020 07:35:57: 8000000 INFO @ Wed, 22 Apr 2020 07:35:57: 14000000 INFO @ Wed, 22 Apr 2020 07:36:02: 9000000 INFO @ Wed, 22 Apr 2020 07:36:03: 15000000 INFO @ Wed, 22 Apr 2020 07:36:07: 10000000 INFO @ Wed, 22 Apr 2020 07:36:08: 16000000 INFO @ Wed, 22 Apr 2020 07:36:11: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:36:11: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:36:11: #1 total tags in treatment: 16536667 INFO @ Wed, 22 Apr 2020 07:36:11: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:36:11: #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 07:36:11: #1 tags after filtering in treatment: 16536495 INFO @ Wed, 22 Apr 2020 07:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:36:11: #1 finished! INFO @ Wed, 22 Apr 2020 07:36:11: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:36:12: 11000000 INFO @ Wed, 22 Apr 2020 07:36:13: #2 number of paired peaks: 3577 INFO @ Wed, 22 Apr 2020 07:36:13: start model_add_line... INFO @ Wed, 22 Apr 2020 07:36:13: start X-correlation... INFO @ Wed, 22 Apr 2020 07:36:13: end of X-cor INFO @ Wed, 22 Apr 2020 07:36:13: #2 finished! INFO @ Wed, 22 Apr 2020 07:36:13: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 07:36:13: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 07:36:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.10_model.r WARNING @ Wed, 22 Apr 2020 07:36:13: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:36:13: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 22 Apr 2020 07:36:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:36:13: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:36:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:36:18: 12000000 INFO @ Wed, 22 Apr 2020 07:36:23: 13000000 INFO @ Wed, 22 Apr 2020 07:36:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:36:28: 14000000 INFO @ Wed, 22 Apr 2020 07:36:33: 15000000 INFO @ Wed, 22 Apr 2020 07:36:39: 16000000 INFO @ Wed, 22 Apr 2020 07:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:36:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:36:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.05_summits.bed INFO @ Wed, 22 Apr 2020 07:36:41: Done! pass1 - making usageList (42 chroms): 2 millis pass2 - checking and writing primary data (864 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:36:42: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:36:42: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:36:42: #1 total tags in treatment: 16536667 INFO @ Wed, 22 Apr 2020 07:36:42: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:36:42: #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 07:36:42: #1 tags after filtering in treatment: 16536495 INFO @ Wed, 22 Apr 2020 07:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:36:42: #1 finished! INFO @ Wed, 22 Apr 2020 07:36:42: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:36:43: #2 number of paired peaks: 3577 INFO @ Wed, 22 Apr 2020 07:36:43: start model_add_line... INFO @ Wed, 22 Apr 2020 07:36:44: start X-correlation... INFO @ Wed, 22 Apr 2020 07:36:44: end of X-cor INFO @ Wed, 22 Apr 2020 07:36:44: #2 finished! INFO @ Wed, 22 Apr 2020 07:36:44: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 07:36:44: #2 alternative fragment length(s) may be 73 bps INFO @ Wed, 22 Apr 2020 07:36:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.20_model.r WARNING @ Wed, 22 Apr 2020 07:36:44: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:36:44: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Wed, 22 Apr 2020 07:36:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:36:44: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:36:50: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:37:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:37:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:37:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.10_summits.bed INFO @ Wed, 22 Apr 2020 07:37:07: Done! pass1 - making usageList (35 chroms): 0 millis pass2 - checking and writing primary data (523 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:37:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:37:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:37:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:37:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625153/SRX7625153.20_summits.bed INFO @ Wed, 22 Apr 2020 07:37:39: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。