Job ID = 5790628 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:18:13 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 ) 2020-04-21T19:18:13 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 : 122,531,281 reads read : 122,531,281 reads written : 122,531,281 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: 00:00:01 Multiseed full-index search: 00:45:19 122531281 reads; of these: 122531281 (100.00%) were unpaired; of these: 2112260 (1.72%) aligned 0 times 107229344 (87.51%) aligned exactly 1 time 13189677 (10.76%) aligned >1 times 98.28% overall alignment rate Time searching: 00:45:20 Overall time: 00:45:20 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 52 files... [bam_rmdupse_core] 75040464 / 120419021 = 0.6232 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 06:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.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 06:23:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:23:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:24:05: 1000000 INFO @ Wed, 22 Apr 2020 06:24:11: 2000000 INFO @ Wed, 22 Apr 2020 06:24:17: 3000000 INFO @ Wed, 22 Apr 2020 06:24:22: 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 06:24:28: 5000000 INFO @ Wed, 22 Apr 2020 06:24:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.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 06:24:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:24:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:24:34: 6000000 INFO @ Wed, 22 Apr 2020 06:24:36: 1000000 INFO @ Wed, 22 Apr 2020 06:24:41: 7000000 INFO @ Wed, 22 Apr 2020 06:24:43: 2000000 INFO @ Wed, 22 Apr 2020 06:24:48: 8000000 INFO @ Wed, 22 Apr 2020 06:24:49: 3000000 INFO @ Wed, 22 Apr 2020 06:24:54: 9000000 INFO @ Wed, 22 Apr 2020 06:24:56: 4000000 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 06:24:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.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 06:24:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 06:24:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 06:25:01: 10000000 INFO @ Wed, 22 Apr 2020 06:25:02: 5000000 INFO @ Wed, 22 Apr 2020 06:25:06: 1000000 INFO @ Wed, 22 Apr 2020 06:25:08: 11000000 INFO @ Wed, 22 Apr 2020 06:25:09: 6000000 INFO @ Wed, 22 Apr 2020 06:25:13: 2000000 INFO @ Wed, 22 Apr 2020 06:25:14: 12000000 INFO @ Wed, 22 Apr 2020 06:25:16: 7000000 INFO @ Wed, 22 Apr 2020 06:25:19: 3000000 INFO @ Wed, 22 Apr 2020 06:25:21: 13000000 INFO @ Wed, 22 Apr 2020 06:25:22: 8000000 INFO @ Wed, 22 Apr 2020 06:25:26: 4000000 INFO @ Wed, 22 Apr 2020 06:25:28: 14000000 INFO @ Wed, 22 Apr 2020 06:25:29: 9000000 INFO @ Wed, 22 Apr 2020 06:25:33: 5000000 INFO @ Wed, 22 Apr 2020 06:25:34: 15000000 INFO @ Wed, 22 Apr 2020 06:25:36: 10000000 INFO @ Wed, 22 Apr 2020 06:25:39: 6000000 INFO @ Wed, 22 Apr 2020 06:25:41: 16000000 INFO @ Wed, 22 Apr 2020 06:25:42: 11000000 INFO @ Wed, 22 Apr 2020 06:25:46: 7000000 INFO @ Wed, 22 Apr 2020 06:25:48: 17000000 INFO @ Wed, 22 Apr 2020 06:25:49: 12000000 INFO @ Wed, 22 Apr 2020 06:25:53: 8000000 INFO @ Wed, 22 Apr 2020 06:25:54: 18000000 INFO @ Wed, 22 Apr 2020 06:25:56: 13000000 INFO @ Wed, 22 Apr 2020 06:26:00: 9000000 INFO @ Wed, 22 Apr 2020 06:26:01: 19000000 INFO @ Wed, 22 Apr 2020 06:26:03: 14000000 INFO @ Wed, 22 Apr 2020 06:26:06: 10000000 INFO @ Wed, 22 Apr 2020 06:26:08: 20000000 INFO @ Wed, 22 Apr 2020 06:26:09: 15000000 INFO @ Wed, 22 Apr 2020 06:26:13: 11000000 INFO @ Wed, 22 Apr 2020 06:26:14: 21000000 INFO @ Wed, 22 Apr 2020 06:26:16: 16000000 INFO @ Wed, 22 Apr 2020 06:26:20: 12000000 INFO @ Wed, 22 Apr 2020 06:26:21: 22000000 INFO @ Wed, 22 Apr 2020 06:26:23: 17000000 INFO @ Wed, 22 Apr 2020 06:26:26: 13000000 INFO @ Wed, 22 Apr 2020 06:26:28: 23000000 INFO @ Wed, 22 Apr 2020 06:26:29: 18000000 INFO @ Wed, 22 Apr 2020 06:26:33: 14000000 INFO @ Wed, 22 Apr 2020 06:26:34: 24000000 INFO @ Wed, 22 Apr 2020 06:26:36: 19000000 INFO @ Wed, 22 Apr 2020 06:26:40: 15000000 INFO @ Wed, 22 Apr 2020 06:26:41: 25000000 INFO @ Wed, 22 Apr 2020 06:26:43: 20000000 INFO @ Wed, 22 Apr 2020 06:26:46: 16000000 INFO @ Wed, 22 Apr 2020 06:26:48: 26000000 INFO @ Wed, 22 Apr 2020 06:26:50: 21000000 INFO @ Wed, 22 Apr 2020 06:26:53: 17000000 INFO @ Wed, 22 Apr 2020 06:26:54: 27000000 INFO @ Wed, 22 Apr 2020 06:26:56: 22000000 INFO @ Wed, 22 Apr 2020 06:27:00: 18000000 INFO @ Wed, 22 Apr 2020 06:27:01: 28000000 INFO @ Wed, 22 Apr 2020 06:27:03: 23000000 INFO @ Wed, 22 Apr 2020 06:27:07: 19000000 INFO @ Wed, 22 Apr 2020 06:27:08: 29000000 INFO @ Wed, 22 Apr 2020 06:27:10: 24000000 INFO @ Wed, 22 Apr 2020 06:27:13: 20000000 INFO @ Wed, 22 Apr 2020 06:27:14: 30000000 INFO @ Wed, 22 Apr 2020 06:27:17: 25000000 INFO @ Wed, 22 Apr 2020 06:27:20: 21000000 INFO @ Wed, 22 Apr 2020 06:27:21: 31000000 INFO @ Wed, 22 Apr 2020 06:27:23: 26000000 INFO @ Wed, 22 Apr 2020 06:27:27: 22000000 INFO @ Wed, 22 Apr 2020 06:27:28: 32000000 INFO @ Wed, 22 Apr 2020 06:27:30: 27000000 INFO @ Wed, 22 Apr 2020 06:27:33: 23000000 INFO @ Wed, 22 Apr 2020 06:27:34: 33000000 INFO @ Wed, 22 Apr 2020 06:27:36: 28000000 INFO @ Wed, 22 Apr 2020 06:27:40: 24000000 INFO @ Wed, 22 Apr 2020 06:27:41: 34000000 INFO @ Wed, 22 Apr 2020 06:27:43: 29000000 INFO @ Wed, 22 Apr 2020 06:27:47: 25000000 INFO @ Wed, 22 Apr 2020 06:27:48: 35000000 INFO @ Wed, 22 Apr 2020 06:27:50: 30000000 INFO @ Wed, 22 Apr 2020 06:27:53: 26000000 INFO @ Wed, 22 Apr 2020 06:27:54: 36000000 INFO @ Wed, 22 Apr 2020 06:27:56: 31000000 INFO @ Wed, 22 Apr 2020 06:28:00: 27000000 INFO @ Wed, 22 Apr 2020 06:28:01: 37000000 INFO @ Wed, 22 Apr 2020 06:28:03: 32000000 INFO @ Wed, 22 Apr 2020 06:28:07: 28000000 INFO @ Wed, 22 Apr 2020 06:28:08: 38000000 INFO @ Wed, 22 Apr 2020 06:28:10: 33000000 INFO @ Wed, 22 Apr 2020 06:28:13: 29000000 INFO @ Wed, 22 Apr 2020 06:28:14: 39000000 INFO @ Wed, 22 Apr 2020 06:28:16: 34000000 INFO @ Wed, 22 Apr 2020 06:28:20: 30000000 INFO @ Wed, 22 Apr 2020 06:28:21: 40000000 INFO @ Wed, 22 Apr 2020 06:28:23: 35000000 INFO @ Wed, 22 Apr 2020 06:28:27: 31000000 INFO @ Wed, 22 Apr 2020 06:28:28: 41000000 INFO @ Wed, 22 Apr 2020 06:28:30: 36000000 INFO @ Wed, 22 Apr 2020 06:28:33: 32000000 INFO @ Wed, 22 Apr 2020 06:28:34: 42000000 INFO @ Wed, 22 Apr 2020 06:28:36: 37000000 INFO @ Wed, 22 Apr 2020 06:28:40: 33000000 INFO @ Wed, 22 Apr 2020 06:28:41: 43000000 INFO @ Wed, 22 Apr 2020 06:28:43: 38000000 INFO @ Wed, 22 Apr 2020 06:28:47: 34000000 INFO @ Wed, 22 Apr 2020 06:28:48: 44000000 INFO @ Wed, 22 Apr 2020 06:28:50: 39000000 INFO @ Wed, 22 Apr 2020 06:28:53: 35000000 INFO @ Wed, 22 Apr 2020 06:28:55: 45000000 INFO @ Wed, 22 Apr 2020 06:28:56: 40000000 INFO @ Wed, 22 Apr 2020 06:28:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 06:28:57: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 06:28:57: #1 total tags in treatment: 45378557 INFO @ Wed, 22 Apr 2020 06:28:57: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:28:57: #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 06:28:58: #1 tags after filtering in treatment: 45378384 INFO @ Wed, 22 Apr 2020 06:28:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:28:58: #1 finished! INFO @ Wed, 22 Apr 2020 06:28:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:28:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:00: 36000000 INFO @ Wed, 22 Apr 2020 06:29:03: 41000000 INFO @ Wed, 22 Apr 2020 06:29:07: 37000000 INFO @ Wed, 22 Apr 2020 06:29:07: #2 number of paired peaks: 111378 INFO @ Wed, 22 Apr 2020 06:29:07: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:08: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:08: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:08: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:08: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 06:29:08: #2 alternative fragment length(s) may be 3,129 bps INFO @ Wed, 22 Apr 2020 06:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.05_model.r INFO @ Wed, 22 Apr 2020 06:29:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:09: 42000000 INFO @ Wed, 22 Apr 2020 06:29:13: 38000000 INFO @ Wed, 22 Apr 2020 06:29:16: 43000000 INFO @ Wed, 22 Apr 2020 06:29:20: 39000000 INFO @ Wed, 22 Apr 2020 06:29:22: 44000000 INFO @ Wed, 22 Apr 2020 06:29:26: 40000000 INFO @ Wed, 22 Apr 2020 06:29:29: 45000000 INFO @ Wed, 22 Apr 2020 06:29:32: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 06:29:32: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 06:29:32: #1 total tags in treatment: 45378557 INFO @ Wed, 22 Apr 2020 06:29:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:32: #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 06:29:33: 41000000 INFO @ Wed, 22 Apr 2020 06:29:33: #1 tags after filtering in treatment: 45378384 INFO @ Wed, 22 Apr 2020 06:29:33: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:29:33: #1 finished! INFO @ Wed, 22 Apr 2020 06:29:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:29:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:29:39: 42000000 INFO @ Wed, 22 Apr 2020 06:29:41: #2 number of paired peaks: 111378 INFO @ Wed, 22 Apr 2020 06:29:41: start model_add_line... INFO @ Wed, 22 Apr 2020 06:29:42: start X-correlation... INFO @ Wed, 22 Apr 2020 06:29:42: end of X-cor INFO @ Wed, 22 Apr 2020 06:29:42: #2 finished! INFO @ Wed, 22 Apr 2020 06:29:42: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 06:29:42: #2 alternative fragment length(s) may be 3,129 bps INFO @ Wed, 22 Apr 2020 06:29:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.10_model.r INFO @ Wed, 22 Apr 2020 06:29:42: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:29:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:29:45: 43000000 INFO @ Wed, 22 Apr 2020 06:29:51: 44000000 INFO @ Wed, 22 Apr 2020 06:29:57: 45000000 INFO @ Wed, 22 Apr 2020 06:29:59: #1 tag size is determined as 50 bps INFO @ Wed, 22 Apr 2020 06:29:59: #1 tag size = 50 INFO @ Wed, 22 Apr 2020 06:29:59: #1 total tags in treatment: 45378557 INFO @ Wed, 22 Apr 2020 06:29:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 06:29:59: #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 06:30:00: #1 tags after filtering in treatment: 45378384 INFO @ Wed, 22 Apr 2020 06:30:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 06:30:00: #1 finished! INFO @ Wed, 22 Apr 2020 06:30:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 06:30:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 06:30:08: #2 number of paired peaks: 111378 INFO @ Wed, 22 Apr 2020 06:30:08: start model_add_line... INFO @ Wed, 22 Apr 2020 06:30:09: start X-correlation... INFO @ Wed, 22 Apr 2020 06:30:09: end of X-cor INFO @ Wed, 22 Apr 2020 06:30:09: #2 finished! INFO @ Wed, 22 Apr 2020 06:30:09: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Apr 2020 06:30:09: #2 alternative fragment length(s) may be 3,129 bps INFO @ Wed, 22 Apr 2020 06:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.20_model.r INFO @ Wed, 22 Apr 2020 06:30:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 06:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 06:30:49: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:31:23: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:31:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.05_peaks.xls INFO @ Wed, 22 Apr 2020 06:31:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:31:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.05_summits.bed INFO @ Wed, 22 Apr 2020 06:31:49: Done! pass1 - making usageList (199 chroms): 13 millis pass2 - checking and writing primary data (90335 records, 4 fields): 84 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 06:31:51: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 06:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.10_peaks.xls INFO @ Wed, 22 Apr 2020 06:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.10_summits.bed INFO @ Wed, 22 Apr 2020 06:32:22: Done! pass1 - making usageList (167 chroms): 9 millis pass2 - checking and writing primary data (68034 records, 4 fields): 64 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 06:32:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.20_peaks.xls INFO @ Wed, 22 Apr 2020 06:32:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 06:32:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101905/ERX101905.20_summits.bed INFO @ Wed, 22 Apr 2020 06:32:49: Done! pass1 - making usageList (133 chroms): 6 millis pass2 - checking and writing primary data (45192 records, 4 fields): 44 millis CompletedMACS2peakCalling BigWig に変換しました。