Job ID = 5790656 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T20:08:26 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 ) 2020-01-00T20:08:26 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 ) 2020-04-21T20:15:39 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 : 45,982,966 reads read : 91,965,932 reads written : 45,982,966 reads 0-length : 45,982,966 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:30:32 45982966 reads; of these: 45982966 (100.00%) were unpaired; of these: 3857850 (8.39%) aligned 0 times 30788600 (66.96%) aligned exactly 1 time 11336516 (24.65%) aligned >1 times 91.61% overall alignment rate Time searching: 00:30:37 Overall time: 00:30:37 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 20 files... [bam_rmdupse_core] 3920913 / 42125116 = 0.0931 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 05:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.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 05:57:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:57:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:57:40: 1000000 INFO @ Wed, 22 Apr 2020 05:57:45: 2000000 INFO @ Wed, 22 Apr 2020 05:57:50: 3000000 INFO @ Wed, 22 Apr 2020 05:57:55: 4000000 INFO @ Wed, 22 Apr 2020 05:58:00: 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 05:58:05: 6000000 INFO @ Wed, 22 Apr 2020 05:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.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 05:58:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:58:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:58:10: 7000000 INFO @ Wed, 22 Apr 2020 05:58:10: 1000000 INFO @ Wed, 22 Apr 2020 05:58:15: 8000000 INFO @ Wed, 22 Apr 2020 05:58:16: 2000000 INFO @ Wed, 22 Apr 2020 05:58:20: 9000000 INFO @ Wed, 22 Apr 2020 05:58:21: 3000000 INFO @ Wed, 22 Apr 2020 05:58:26: 10000000 INFO @ Wed, 22 Apr 2020 05:58:26: 4000000 INFO @ Wed, 22 Apr 2020 05:58:31: 11000000 INFO @ Wed, 22 Apr 2020 05:58:31: 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 05:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.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 05:58:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:58:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:58:36: 12000000 INFO @ Wed, 22 Apr 2020 05:58:37: 6000000 INFO @ Wed, 22 Apr 2020 05:58:40: 1000000 INFO @ Wed, 22 Apr 2020 05:58:42: 13000000 INFO @ Wed, 22 Apr 2020 05:58:42: 7000000 INFO @ Wed, 22 Apr 2020 05:58:46: 2000000 INFO @ Wed, 22 Apr 2020 05:58:47: 14000000 INFO @ Wed, 22 Apr 2020 05:58:48: 8000000 INFO @ Wed, 22 Apr 2020 05:58:51: 3000000 INFO @ Wed, 22 Apr 2020 05:58:52: 15000000 INFO @ Wed, 22 Apr 2020 05:58:53: 9000000 INFO @ Wed, 22 Apr 2020 05:58:57: 4000000 INFO @ Wed, 22 Apr 2020 05:58:58: 16000000 INFO @ Wed, 22 Apr 2020 05:58:59: 10000000 INFO @ Wed, 22 Apr 2020 05:59:02: 5000000 INFO @ Wed, 22 Apr 2020 05:59:03: 17000000 INFO @ Wed, 22 Apr 2020 05:59:04: 11000000 INFO @ Wed, 22 Apr 2020 05:59:07: 6000000 INFO @ Wed, 22 Apr 2020 05:59:08: 18000000 INFO @ Wed, 22 Apr 2020 05:59:09: 12000000 INFO @ Wed, 22 Apr 2020 05:59:13: 7000000 INFO @ Wed, 22 Apr 2020 05:59:14: 19000000 INFO @ Wed, 22 Apr 2020 05:59:15: 13000000 INFO @ Wed, 22 Apr 2020 05:59:18: 8000000 INFO @ Wed, 22 Apr 2020 05:59:19: 20000000 INFO @ Wed, 22 Apr 2020 05:59:20: 14000000 INFO @ Wed, 22 Apr 2020 05:59:24: 9000000 INFO @ Wed, 22 Apr 2020 05:59:24: 21000000 INFO @ Wed, 22 Apr 2020 05:59:25: 15000000 INFO @ Wed, 22 Apr 2020 05:59:29: 10000000 INFO @ Wed, 22 Apr 2020 05:59:30: 22000000 INFO @ Wed, 22 Apr 2020 05:59:31: 16000000 INFO @ Wed, 22 Apr 2020 05:59:34: 11000000 INFO @ Wed, 22 Apr 2020 05:59:35: 23000000 INFO @ Wed, 22 Apr 2020 05:59:36: 17000000 INFO @ Wed, 22 Apr 2020 05:59:40: 12000000 INFO @ Wed, 22 Apr 2020 05:59:40: 24000000 INFO @ Wed, 22 Apr 2020 05:59:41: 18000000 INFO @ Wed, 22 Apr 2020 05:59:45: 13000000 INFO @ Wed, 22 Apr 2020 05:59:46: 25000000 INFO @ Wed, 22 Apr 2020 05:59:47: 19000000 INFO @ Wed, 22 Apr 2020 05:59:50: 14000000 INFO @ Wed, 22 Apr 2020 05:59:51: 26000000 INFO @ Wed, 22 Apr 2020 05:59:52: 20000000 INFO @ Wed, 22 Apr 2020 05:59:56: 15000000 INFO @ Wed, 22 Apr 2020 05:59:56: 27000000 INFO @ Wed, 22 Apr 2020 05:59:57: 21000000 INFO @ Wed, 22 Apr 2020 06:00:01: 16000000 INFO @ Wed, 22 Apr 2020 06:00:02: 28000000 INFO @ Wed, 22 Apr 2020 06:00:03: 22000000 INFO @ Wed, 22 Apr 2020 06:00:06: 17000000 INFO @ Wed, 22 Apr 2020 06:00:07: 29000000 INFO @ Wed, 22 Apr 2020 06:00:08: 23000000 INFO @ Wed, 22 Apr 2020 06:00:11: 18000000 INFO @ Wed, 22 Apr 2020 06:00:12: 30000000 INFO @ Wed, 22 Apr 2020 06:00:13: 24000000 INFO @ Wed, 22 Apr 2020 06:00:17: 19000000 INFO @ Wed, 22 Apr 2020 06:00:18: 31000000 INFO @ Wed, 22 Apr 2020 06:00:19: 25000000 INFO @ Wed, 22 Apr 2020 06:00:22: 20000000 INFO @ Wed, 22 Apr 2020 06:00:23: 32000000 INFO @ Wed, 22 Apr 2020 06:00:24: 26000000 INFO @ Wed, 22 Apr 2020 06:00:27: 21000000 INFO @ Wed, 22 Apr 2020 06:00:28: 33000000 INFO @ Wed, 22 Apr 2020 06:00:29: 27000000 INFO @ Wed, 22 Apr 2020 06:00:33: 22000000 INFO @ Wed, 22 Apr 2020 06:00:33: 34000000 INFO @ Wed, 22 Apr 2020 06:00:35: 28000000 INFO @ Wed, 22 Apr 2020 06:00:38: 23000000 INFO @ Wed, 22 Apr 2020 06:00:39: 35000000 INFO @ Wed, 22 Apr 2020 06:00:40: 29000000 INFO @ Wed, 22 Apr 2020 06:00:43: 24000000 INFO @ Wed, 22 Apr 2020 06:00:44: 36000000 INFO @ Wed, 22 Apr 2020 06:00:45: 30000000 INFO @ Wed, 22 Apr 2020 06:00:48: 25000000 INFO @ Wed, 22 Apr 2020 06:00:49: 37000000 INFO @ Wed, 22 Apr 2020 06:00:50: 31000000 INFO @ Wed, 22 Apr 2020 06:00:54: 26000000 INFO @ Wed, 22 Apr 2020 06:00:55: 38000000 INFO @ Wed, 22 Apr 2020 06:00:56: 32000000 INFO @ Wed, 22 Apr 2020 06:00:56: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:00:56: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:00:56: #1 total tags in treatment: 38204203 INFO @ Wed, 22 Apr 2020 06:00:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:00:56: #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 06:00:57: #1 tags after filtering in treatment: 38204129 INFO @ Wed, 22 Apr 2020 06:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:00:57: #1 finished! INFO @ Wed, 22 Apr 2020 06:00:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:00:59: 27000000 INFO @ Wed, 22 Apr 2020 06:01:00: #2 number of paired peaks: 20415 INFO @ Wed, 22 Apr 2020 06:01:00: start model_add_line... INFO @ Wed, 22 Apr 2020 06:01:01: start X-correlation... INFO @ Wed, 22 Apr 2020 06:01:01: end of X-cor INFO @ Wed, 22 Apr 2020 06:01:01: #2 finished! INFO @ Wed, 22 Apr 2020 06:01:01: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Apr 2020 06:01:01: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 22 Apr 2020 06:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.05_model.r INFO @ Wed, 22 Apr 2020 06:01:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:01:01: 33000000 INFO @ Wed, 22 Apr 2020 06:01:04: 28000000 INFO @ Wed, 22 Apr 2020 06:01:06: 34000000 INFO @ Wed, 22 Apr 2020 06:01:09: 29000000 INFO @ Wed, 22 Apr 2020 06:01:12: 35000000 INFO @ Wed, 22 Apr 2020 06:01:15: 30000000 INFO @ Wed, 22 Apr 2020 06:01:17: 36000000 INFO @ Wed, 22 Apr 2020 06:01:20: 31000000 INFO @ Wed, 22 Apr 2020 06:01:22: 37000000 INFO @ Wed, 22 Apr 2020 06:01:25: 32000000 INFO @ Wed, 22 Apr 2020 06:01:28: 38000000 INFO @ Wed, 22 Apr 2020 06:01:29: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:01:29: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:01:29: #1 total tags in treatment: 38204203 INFO @ Wed, 22 Apr 2020 06:01:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:01:29: #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 06:01:30: #1 tags after filtering in treatment: 38204129 INFO @ Wed, 22 Apr 2020 06:01:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:01:30: #1 finished! INFO @ Wed, 22 Apr 2020 06:01:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:01:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:01:30: 33000000 INFO @ Wed, 22 Apr 2020 06:01:33: #2 number of paired peaks: 20415 INFO @ Wed, 22 Apr 2020 06:01:33: start model_add_line... INFO @ Wed, 22 Apr 2020 06:01:34: start X-correlation... INFO @ Wed, 22 Apr 2020 06:01:34: end of X-cor INFO @ Wed, 22 Apr 2020 06:01:34: #2 finished! INFO @ Wed, 22 Apr 2020 06:01:34: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Apr 2020 06:01:34: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 22 Apr 2020 06:01:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.10_model.r INFO @ Wed, 22 Apr 2020 06:01:34: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:01:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:01:36: 34000000 INFO @ Wed, 22 Apr 2020 06:01:41: 35000000 INFO @ Wed, 22 Apr 2020 06:01:46: 36000000 INFO @ Wed, 22 Apr 2020 06:01:51: 37000000 INFO @ Wed, 22 Apr 2020 06:01:56: 38000000 INFO @ Wed, 22 Apr 2020 06:01:58: #1 tag size is determined as 51 bps INFO @ Wed, 22 Apr 2020 06:01:58: #1 tag size = 51 INFO @ Wed, 22 Apr 2020 06:01:58: #1 total tags in treatment: 38204203 INFO @ Wed, 22 Apr 2020 06:01:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:01:58: #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 06:01:58: #1 tags after filtering in treatment: 38204129 INFO @ Wed, 22 Apr 2020 06:01:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:01:58: #1 finished! INFO @ Wed, 22 Apr 2020 06:01:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:02:02: #2 number of paired peaks: 20415 INFO @ Wed, 22 Apr 2020 06:02:02: start model_add_line... INFO @ Wed, 22 Apr 2020 06:02:02: start X-correlation... INFO @ Wed, 22 Apr 2020 06:02:02: end of X-cor INFO @ Wed, 22 Apr 2020 06:02:02: #2 finished! INFO @ Wed, 22 Apr 2020 06:02:02: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Apr 2020 06:02:02: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 22 Apr 2020 06:02:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.20_model.r INFO @ Wed, 22 Apr 2020 06:02:02: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:02:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:02:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:02:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.05_summits.bed INFO @ Wed, 22 Apr 2020 06:03:15: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (11094 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:03:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.10_summits.bed INFO @ Wed, 22 Apr 2020 06:03:45: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (4025 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5433267/SRX5433267.20_summits.bed INFO @ Wed, 22 Apr 2020 06:04:11: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1048 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。