Job ID = 5720774 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:24:20 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 ) 2020-04-15T16:24:20 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 ) 2020-04-15T16:30:54 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 ) 2020-04-15T16:30:54 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 ) 2020-04-15T16:40:42 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 ) 2020-04-15T16:43:41 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 : 24,017,657 reads read : 48,035,314 reads written : 48,035,314 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: 02:25:02 24017657 reads; of these: 24017657 (100.00%) were paired; of these: 5977200 (24.89%) aligned concordantly 0 times 5792298 (24.12%) aligned concordantly exactly 1 time 12248159 (51.00%) aligned concordantly >1 times ---- 5977200 pairs aligned concordantly 0 times; of these: 759402 (12.70%) aligned discordantly 1 time ---- 5217798 pairs aligned 0 times concordantly or discordantly; of these: 10435596 mates make up the pairs; of these: 3561207 (34.13%) aligned 0 times 852213 (8.17%) aligned exactly 1 time 6022176 (57.71%) aligned >1 times 92.59% overall alignment rate Time searching: 02:25:02 Overall time: 02:25:03 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_sort_core] merging from 20 files... [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] 2589661 / 18703661 = 0.1385 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 04:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.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 04:29:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:29:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:29:08: 1000000 INFO @ Thu, 16 Apr 2020 04:29:16: 2000000 INFO @ Thu, 16 Apr 2020 04:29:23: 3000000 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 04:29:30: 4000000 INFO @ Thu, 16 Apr 2020 04:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.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 04:29:31: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:29:31: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:29:38: 1000000 INFO @ Thu, 16 Apr 2020 04:29:38: 5000000 INFO @ Thu, 16 Apr 2020 04:29:45: 2000000 INFO @ Thu, 16 Apr 2020 04:29:46: 6000000 INFO @ Thu, 16 Apr 2020 04:29:52: 3000000 INFO @ Thu, 16 Apr 2020 04:29:53: 7000000 INFO @ Thu, 16 Apr 2020 04:29:59: 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 @ Thu, 16 Apr 2020 04:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.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 04:30:01: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:30:01: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:30:01: 8000000 INFO @ Thu, 16 Apr 2020 04:30:06: 5000000 INFO @ Thu, 16 Apr 2020 04:30:08: 1000000 INFO @ Thu, 16 Apr 2020 04:30:08: 9000000 INFO @ Thu, 16 Apr 2020 04:30:13: 6000000 INFO @ Thu, 16 Apr 2020 04:30:15: 2000000 INFO @ Thu, 16 Apr 2020 04:30:16: 10000000 INFO @ Thu, 16 Apr 2020 04:30:20: 7000000 INFO @ Thu, 16 Apr 2020 04:30:22: 3000000 INFO @ Thu, 16 Apr 2020 04:30:23: 11000000 INFO @ Thu, 16 Apr 2020 04:30:27: 8000000 INFO @ Thu, 16 Apr 2020 04:30:29: 4000000 INFO @ Thu, 16 Apr 2020 04:30:31: 12000000 INFO @ Thu, 16 Apr 2020 04:30:33: 9000000 INFO @ Thu, 16 Apr 2020 04:30:36: 5000000 INFO @ Thu, 16 Apr 2020 04:30:38: 13000000 INFO @ Thu, 16 Apr 2020 04:30:40: 10000000 INFO @ Thu, 16 Apr 2020 04:30:43: 6000000 INFO @ Thu, 16 Apr 2020 04:30:46: 14000000 INFO @ Thu, 16 Apr 2020 04:30:47: 11000000 INFO @ Thu, 16 Apr 2020 04:30:50: 7000000 INFO @ Thu, 16 Apr 2020 04:30:53: 15000000 INFO @ Thu, 16 Apr 2020 04:30:54: 12000000 INFO @ Thu, 16 Apr 2020 04:30:57: 8000000 INFO @ Thu, 16 Apr 2020 04:31:01: 16000000 INFO @ Thu, 16 Apr 2020 04:31:01: 13000000 INFO @ Thu, 16 Apr 2020 04:31:04: 9000000 INFO @ Thu, 16 Apr 2020 04:31:08: 14000000 INFO @ Thu, 16 Apr 2020 04:31:08: 17000000 INFO @ Thu, 16 Apr 2020 04:31:10: 10000000 INFO @ Thu, 16 Apr 2020 04:31:15: 15000000 INFO @ Thu, 16 Apr 2020 04:31:16: 18000000 INFO @ Thu, 16 Apr 2020 04:31:17: 11000000 INFO @ Thu, 16 Apr 2020 04:31:22: 16000000 INFO @ Thu, 16 Apr 2020 04:31:24: 19000000 INFO @ Thu, 16 Apr 2020 04:31:24: 12000000 INFO @ Thu, 16 Apr 2020 04:31:28: 17000000 INFO @ Thu, 16 Apr 2020 04:31:31: 13000000 INFO @ Thu, 16 Apr 2020 04:31:32: 20000000 INFO @ Thu, 16 Apr 2020 04:31:35: 18000000 INFO @ Thu, 16 Apr 2020 04:31:38: 14000000 INFO @ Thu, 16 Apr 2020 04:31:39: 21000000 INFO @ Thu, 16 Apr 2020 04:31:42: 19000000 INFO @ Thu, 16 Apr 2020 04:31:44: 15000000 INFO @ Thu, 16 Apr 2020 04:31:47: 22000000 INFO @ Thu, 16 Apr 2020 04:31:49: 20000000 INFO @ Thu, 16 Apr 2020 04:31:51: 16000000 INFO @ Thu, 16 Apr 2020 04:31:55: 23000000 INFO @ Thu, 16 Apr 2020 04:31:56: 21000000 INFO @ Thu, 16 Apr 2020 04:31:58: 17000000 INFO @ Thu, 16 Apr 2020 04:32:02: 24000000 INFO @ Thu, 16 Apr 2020 04:32:03: 22000000 INFO @ Thu, 16 Apr 2020 04:32:05: 18000000 INFO @ Thu, 16 Apr 2020 04:32:10: 25000000 INFO @ Thu, 16 Apr 2020 04:32:10: 23000000 INFO @ Thu, 16 Apr 2020 04:32:12: 19000000 INFO @ Thu, 16 Apr 2020 04:32:17: 24000000 INFO @ Thu, 16 Apr 2020 04:32:17: 26000000 INFO @ Thu, 16 Apr 2020 04:32:19: 20000000 INFO @ Thu, 16 Apr 2020 04:32:24: 25000000 INFO @ Thu, 16 Apr 2020 04:32:25: 27000000 INFO @ Thu, 16 Apr 2020 04:32:26: 21000000 INFO @ Thu, 16 Apr 2020 04:32:31: 26000000 INFO @ Thu, 16 Apr 2020 04:32:32: 28000000 INFO @ Thu, 16 Apr 2020 04:32:33: 22000000 INFO @ Thu, 16 Apr 2020 04:32:38: 27000000 INFO @ Thu, 16 Apr 2020 04:32:40: 29000000 INFO @ Thu, 16 Apr 2020 04:32:40: 23000000 INFO @ Thu, 16 Apr 2020 04:32:45: 28000000 INFO @ Thu, 16 Apr 2020 04:32:47: 24000000 INFO @ Thu, 16 Apr 2020 04:32:47: 30000000 INFO @ Thu, 16 Apr 2020 04:32:51: 29000000 INFO @ Thu, 16 Apr 2020 04:32:54: 25000000 INFO @ Thu, 16 Apr 2020 04:32:55: 31000000 INFO @ Thu, 16 Apr 2020 04:32:58: 30000000 INFO @ Thu, 16 Apr 2020 04:33:01: 26000000 INFO @ Thu, 16 Apr 2020 04:33:02: 32000000 INFO @ Thu, 16 Apr 2020 04:33:05: 31000000 INFO @ Thu, 16 Apr 2020 04:33:07: 27000000 INFO @ Thu, 16 Apr 2020 04:33:09: 33000000 INFO @ Thu, 16 Apr 2020 04:33:12: 32000000 INFO @ Thu, 16 Apr 2020 04:33:14: 28000000 INFO @ Thu, 16 Apr 2020 04:33:17: 34000000 INFO @ Thu, 16 Apr 2020 04:33:19: 33000000 INFO @ Thu, 16 Apr 2020 04:33:21: 29000000 INFO @ Thu, 16 Apr 2020 04:33:24: 35000000 INFO @ Thu, 16 Apr 2020 04:33:26: 34000000 INFO @ Thu, 16 Apr 2020 04:33:28: 30000000 INFO @ Thu, 16 Apr 2020 04:33:32: 36000000 INFO @ Thu, 16 Apr 2020 04:33:33: 35000000 INFO @ Thu, 16 Apr 2020 04:33:35: 31000000 INFO @ Thu, 16 Apr 2020 04:33:40: 36000000 INFO @ Thu, 16 Apr 2020 04:33:40: 37000000 INFO @ Thu, 16 Apr 2020 04:33:42: 32000000 INFO @ Thu, 16 Apr 2020 04:33:47: 37000000 INFO @ Thu, 16 Apr 2020 04:33:47: 38000000 INFO @ Thu, 16 Apr 2020 04:33:49: 33000000 INFO @ Thu, 16 Apr 2020 04:33:54: 38000000 INFO @ Thu, 16 Apr 2020 04:33:55: 39000000 INFO @ Thu, 16 Apr 2020 04:33:55: 34000000 INFO @ Thu, 16 Apr 2020 04:33:57: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:33:57: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:33:57: #1 total tags in treatment: 15544939 INFO @ Thu, 16 Apr 2020 04:33:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:33:57: #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 04:33:57: #1 tags after filtering in treatment: 13329093 INFO @ Thu, 16 Apr 2020 04:33:57: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 04:33:57: #1 finished! INFO @ Thu, 16 Apr 2020 04:33:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:33:58: #2 number of paired peaks: 2746 INFO @ Thu, 16 Apr 2020 04:33:58: start model_add_line... INFO @ Thu, 16 Apr 2020 04:33:59: start X-correlation... INFO @ Thu, 16 Apr 2020 04:33:59: end of X-cor INFO @ Thu, 16 Apr 2020 04:33:59: #2 finished! INFO @ Thu, 16 Apr 2020 04:33:59: #2 predicted fragment length is 231 bps INFO @ Thu, 16 Apr 2020 04:33:59: #2 alternative fragment length(s) may be 231 bps INFO @ Thu, 16 Apr 2020 04:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.05_model.r INFO @ Thu, 16 Apr 2020 04:33:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:34:01: 39000000 INFO @ Thu, 16 Apr 2020 04:34:02: 35000000 INFO @ Thu, 16 Apr 2020 04:34:03: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:34:03: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:34:03: #1 total tags in treatment: 15544939 INFO @ Thu, 16 Apr 2020 04:34:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:34:03: #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 04:34:03: #1 tags after filtering in treatment: 13329093 INFO @ Thu, 16 Apr 2020 04:34:03: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 04:34:03: #1 finished! INFO @ Thu, 16 Apr 2020 04:34:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:34:04: #2 number of paired peaks: 2746 INFO @ Thu, 16 Apr 2020 04:34:04: start model_add_line... INFO @ Thu, 16 Apr 2020 04:34:04: start X-correlation... INFO @ Thu, 16 Apr 2020 04:34:04: end of X-cor INFO @ Thu, 16 Apr 2020 04:34:04: #2 finished! INFO @ Thu, 16 Apr 2020 04:34:04: #2 predicted fragment length is 231 bps INFO @ Thu, 16 Apr 2020 04:34:04: #2 alternative fragment length(s) may be 231 bps INFO @ Thu, 16 Apr 2020 04:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.10_model.r INFO @ Thu, 16 Apr 2020 04:34:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:34:09: 36000000 INFO @ Thu, 16 Apr 2020 04:34:15: 37000000 INFO @ Thu, 16 Apr 2020 04:34:22: 38000000 INFO @ Thu, 16 Apr 2020 04:34:28: 39000000 INFO @ Thu, 16 Apr 2020 04:34:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:34:30: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:34:30: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:34:30: #1 total tags in treatment: 15544939 INFO @ Thu, 16 Apr 2020 04:34:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:34:30: #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 04:34:30: #1 tags after filtering in treatment: 13329093 INFO @ Thu, 16 Apr 2020 04:34:30: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 04:34:30: #1 finished! INFO @ Thu, 16 Apr 2020 04:34:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:34:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:34:31: #2 number of paired peaks: 2746 INFO @ Thu, 16 Apr 2020 04:34:31: start model_add_line... INFO @ Thu, 16 Apr 2020 04:34:31: start X-correlation... INFO @ Thu, 16 Apr 2020 04:34:31: end of X-cor INFO @ Thu, 16 Apr 2020 04:34:31: #2 finished! INFO @ Thu, 16 Apr 2020 04:34:31: #2 predicted fragment length is 231 bps INFO @ Thu, 16 Apr 2020 04:34:31: #2 alternative fragment length(s) may be 231 bps INFO @ Thu, 16 Apr 2020 04:34:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.20_model.r INFO @ Thu, 16 Apr 2020 04:34:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:34:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:34:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:34:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:34:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:34:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.05_summits.bed INFO @ Thu, 16 Apr 2020 04:34:47: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (15897 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:34:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:34:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:34:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.10_summits.bed INFO @ Thu, 16 Apr 2020 04:34:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10602 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:35:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246867/SRX5246867.20_summits.bed INFO @ Thu, 16 Apr 2020 04:35:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5587 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。