Job ID = 5790660 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:20:57 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 ) 2020-04-21T20:24:31 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 ) 2020-04-21T20:25:05 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 ) 2020-04-21T20:25:05 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.238' from '172.19.7.189' 2020-04-21T20:25:05 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' (165.112.9.238) from '172.19.7.189' spots read : 37,080,298 reads read : 74,160,596 reads written : 37,080,298 reads 0-length : 37,080,298 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:26 37080298 reads; of these: 37080298 (100.00%) were unpaired; of these: 826349 (2.23%) aligned 0 times 26272698 (70.85%) aligned exactly 1 time 9981251 (26.92%) aligned >1 times 97.77% overall alignment rate Time searching: 00:27:27 Overall time: 00:27:27 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 16 files... [bam_rmdupse_core] 1050388 / 36253949 = 0.0290 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 06:01:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.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 06:01:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:01:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:01:34: 1000000 INFO @ Wed, 22 Apr 2020 06:01:39: 2000000 INFO @ Wed, 22 Apr 2020 06:01:45: 3000000 INFO @ Wed, 22 Apr 2020 06:01:51: 4000000 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 06:01:57: 5000000 INFO @ Wed, 22 Apr 2020 06:01:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.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 06:01:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:01:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:02:03: 6000000 INFO @ Wed, 22 Apr 2020 06:02:04: 1000000 INFO @ Wed, 22 Apr 2020 06:02:10: 7000000 INFO @ Wed, 22 Apr 2020 06:02:10: 2000000 INFO @ Wed, 22 Apr 2020 06:02:16: 8000000 INFO @ Wed, 22 Apr 2020 06:02:17: 3000000 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 06:02:23: 9000000 INFO @ Wed, 22 Apr 2020 06:02:23: 4000000 INFO @ Wed, 22 Apr 2020 06:02:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.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 06:02:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:02:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:02:30: 10000000 INFO @ Wed, 22 Apr 2020 06:02:30: 5000000 INFO @ Wed, 22 Apr 2020 06:02:34: 1000000 INFO @ Wed, 22 Apr 2020 06:02:36: 11000000 INFO @ Wed, 22 Apr 2020 06:02:37: 6000000 INFO @ Wed, 22 Apr 2020 06:02:41: 2000000 INFO @ Wed, 22 Apr 2020 06:02:43: 12000000 INFO @ Wed, 22 Apr 2020 06:02:43: 7000000 INFO @ Wed, 22 Apr 2020 06:02:47: 3000000 INFO @ Wed, 22 Apr 2020 06:02:49: 13000000 INFO @ Wed, 22 Apr 2020 06:02:50: 8000000 INFO @ Wed, 22 Apr 2020 06:02:54: 4000000 INFO @ Wed, 22 Apr 2020 06:02:56: 14000000 INFO @ Wed, 22 Apr 2020 06:02:56: 9000000 INFO @ Wed, 22 Apr 2020 06:03:00: 5000000 INFO @ Wed, 22 Apr 2020 06:03:02: 15000000 INFO @ Wed, 22 Apr 2020 06:03:03: 10000000 INFO @ Wed, 22 Apr 2020 06:03:07: 6000000 INFO @ Wed, 22 Apr 2020 06:03:09: 16000000 INFO @ Wed, 22 Apr 2020 06:03:09: 11000000 INFO @ Wed, 22 Apr 2020 06:03:14: 7000000 INFO @ Wed, 22 Apr 2020 06:03:16: 17000000 INFO @ Wed, 22 Apr 2020 06:03:16: 12000000 INFO @ Wed, 22 Apr 2020 06:03:20: 8000000 INFO @ Wed, 22 Apr 2020 06:03:22: 18000000 INFO @ Wed, 22 Apr 2020 06:03:22: 13000000 INFO @ Wed, 22 Apr 2020 06:03:27: 9000000 INFO @ Wed, 22 Apr 2020 06:03:29: 14000000 INFO @ Wed, 22 Apr 2020 06:03:29: 19000000 INFO @ Wed, 22 Apr 2020 06:03:33: 10000000 INFO @ Wed, 22 Apr 2020 06:03:35: 15000000 INFO @ Wed, 22 Apr 2020 06:03:35: 20000000 INFO @ Wed, 22 Apr 2020 06:03:40: 11000000 INFO @ Wed, 22 Apr 2020 06:03:42: 16000000 INFO @ Wed, 22 Apr 2020 06:03:42: 21000000 INFO @ Wed, 22 Apr 2020 06:03:46: 12000000 INFO @ Wed, 22 Apr 2020 06:03:48: 17000000 INFO @ Wed, 22 Apr 2020 06:03:48: 22000000 INFO @ Wed, 22 Apr 2020 06:03:53: 13000000 INFO @ Wed, 22 Apr 2020 06:03:55: 18000000 INFO @ Wed, 22 Apr 2020 06:03:55: 23000000 INFO @ Wed, 22 Apr 2020 06:03:59: 14000000 INFO @ Wed, 22 Apr 2020 06:04:01: 19000000 INFO @ Wed, 22 Apr 2020 06:04:01: 24000000 INFO @ Wed, 22 Apr 2020 06:04:06: 15000000 INFO @ Wed, 22 Apr 2020 06:04:08: 20000000 INFO @ Wed, 22 Apr 2020 06:04:08: 25000000 INFO @ Wed, 22 Apr 2020 06:04:13: 16000000 INFO @ Wed, 22 Apr 2020 06:04:14: 21000000 INFO @ Wed, 22 Apr 2020 06:04:15: 26000000 INFO @ Wed, 22 Apr 2020 06:04:19: 17000000 INFO @ Wed, 22 Apr 2020 06:04:21: 22000000 INFO @ Wed, 22 Apr 2020 06:04:21: 27000000 INFO @ Wed, 22 Apr 2020 06:04:26: 18000000 INFO @ Wed, 22 Apr 2020 06:04:28: 23000000 INFO @ Wed, 22 Apr 2020 06:04:28: 28000000 INFO @ Wed, 22 Apr 2020 06:04:32: 19000000 INFO @ Wed, 22 Apr 2020 06:04:34: 24000000 INFO @ Wed, 22 Apr 2020 06:04:34: 29000000 INFO @ Wed, 22 Apr 2020 06:04:39: 20000000 INFO @ Wed, 22 Apr 2020 06:04:41: 25000000 INFO @ Wed, 22 Apr 2020 06:04:41: 30000000 INFO @ Wed, 22 Apr 2020 06:04:46: 21000000 INFO @ Wed, 22 Apr 2020 06:04:48: 26000000 INFO @ Wed, 22 Apr 2020 06:04:48: 31000000 INFO @ Wed, 22 Apr 2020 06:04:53: 22000000 INFO @ Wed, 22 Apr 2020 06:04:54: 27000000 INFO @ Wed, 22 Apr 2020 06:04:55: 32000000 INFO @ Wed, 22 Apr 2020 06:05:00: 23000000 INFO @ Wed, 22 Apr 2020 06:05:01: 28000000 INFO @ Wed, 22 Apr 2020 06:05:01: 33000000 INFO @ Wed, 22 Apr 2020 06:05:06: 24000000 INFO @ Wed, 22 Apr 2020 06:05:07: 29000000 INFO @ Wed, 22 Apr 2020 06:05:08: 34000000 INFO @ Wed, 22 Apr 2020 06:05:12: 25000000 INFO @ Wed, 22 Apr 2020 06:05:14: 30000000 INFO @ Wed, 22 Apr 2020 06:05:14: 35000000 INFO @ Wed, 22 Apr 2020 06:05:15: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:05:15: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:05:15: #1 total tags in treatment: 35203561 INFO @ Wed, 22 Apr 2020 06:05:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:05:15: #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 06:05:16: #1 tags after filtering in treatment: 35203476 INFO @ Wed, 22 Apr 2020 06:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:05:16: #1 finished! INFO @ Wed, 22 Apr 2020 06:05:16: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:05:19: 26000000 INFO @ Wed, 22 Apr 2020 06:05:19: #2 number of paired peaks: 4378 INFO @ Wed, 22 Apr 2020 06:05:19: start model_add_line... INFO @ Wed, 22 Apr 2020 06:05:19: start X-correlation... INFO @ Wed, 22 Apr 2020 06:05:19: end of X-cor INFO @ Wed, 22 Apr 2020 06:05:19: #2 finished! INFO @ Wed, 22 Apr 2020 06:05:19: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 06:05:19: #2 alternative fragment length(s) may be 51,212,411 bps INFO @ Wed, 22 Apr 2020 06:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.05_model.r WARNING @ Wed, 22 Apr 2020 06:05:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:05:19: #2 You may need to consider one of the other alternative d(s): 51,212,411 WARNING @ Wed, 22 Apr 2020 06:05:19: #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 06:05:19: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:05:20: 31000000 INFO @ Wed, 22 Apr 2020 06:05:25: 27000000 INFO @ Wed, 22 Apr 2020 06:05:26: 32000000 INFO @ Wed, 22 Apr 2020 06:05:31: 28000000 INFO @ Wed, 22 Apr 2020 06:05:33: 33000000 INFO @ Wed, 22 Apr 2020 06:05:38: 29000000 INFO @ Wed, 22 Apr 2020 06:05:39: 34000000 INFO @ Wed, 22 Apr 2020 06:05:44: 30000000 INFO @ Wed, 22 Apr 2020 06:05:46: 35000000 INFO @ Wed, 22 Apr 2020 06:05:47: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:05:47: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:05:47: #1 total tags in treatment: 35203561 INFO @ Wed, 22 Apr 2020 06:05:47: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:05:47: #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 06:05:48: #1 tags after filtering in treatment: 35203476 INFO @ Wed, 22 Apr 2020 06:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:05:48: #1 finished! INFO @ Wed, 22 Apr 2020 06:05:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:05:50: 31000000 INFO @ Wed, 22 Apr 2020 06:05:51: #2 number of paired peaks: 4378 INFO @ Wed, 22 Apr 2020 06:05:51: start model_add_line... INFO @ Wed, 22 Apr 2020 06:05:51: start X-correlation... INFO @ Wed, 22 Apr 2020 06:05:51: end of X-cor INFO @ Wed, 22 Apr 2020 06:05:51: #2 finished! INFO @ Wed, 22 Apr 2020 06:05:51: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 06:05:51: #2 alternative fragment length(s) may be 51,212,411 bps INFO @ Wed, 22 Apr 2020 06:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.10_model.r WARNING @ Wed, 22 Apr 2020 06:05:51: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:05:51: #2 You may need to consider one of the other alternative d(s): 51,212,411 WARNING @ Wed, 22 Apr 2020 06:05:51: #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 06:05:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:05:56: 32000000 INFO @ Wed, 22 Apr 2020 06:06:02: 33000000 INFO @ Wed, 22 Apr 2020 06:06:08: 34000000 INFO @ Wed, 22 Apr 2020 06:06:13: 35000000 INFO @ Wed, 22 Apr 2020 06:06:15: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:06:15: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:06:15: #1 total tags in treatment: 35203561 INFO @ Wed, 22 Apr 2020 06:06:15: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:06:15: #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 06:06:15: #1 tags after filtering in treatment: 35203476 INFO @ Wed, 22 Apr 2020 06:06:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:06:15: #1 finished! INFO @ Wed, 22 Apr 2020 06:06:15: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:06:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:06:18: #2 number of paired peaks: 4378 INFO @ Wed, 22 Apr 2020 06:06:18: start model_add_line... INFO @ Wed, 22 Apr 2020 06:06:18: start X-correlation... INFO @ Wed, 22 Apr 2020 06:06:18: end of X-cor INFO @ Wed, 22 Apr 2020 06:06:18: #2 finished! INFO @ Wed, 22 Apr 2020 06:06:18: #2 predicted fragment length is 51 bps INFO @ Wed, 22 Apr 2020 06:06:18: #2 alternative fragment length(s) may be 51,212,411 bps INFO @ Wed, 22 Apr 2020 06:06:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.20_model.r WARNING @ Wed, 22 Apr 2020 06:06:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 06:06:18: #2 You may need to consider one of the other alternative d(s): 51,212,411 WARNING @ Wed, 22 Apr 2020 06:06:18: #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 06:06:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:06:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:06:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:07:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:07:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:07:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:07:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.05_summits.bed INFO @ Wed, 22 Apr 2020 06:07:13: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:07:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.10_summits.bed INFO @ Wed, 22 Apr 2020 06:07:45: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1082 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433271/SRX5433271.20_summits.bed INFO @ Wed, 22 Apr 2020 06:08:12: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (541 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。