Job ID = 5721153 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T20:21:49 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 ) 2020-04-15T20:23:04 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 ) 2020-04-15T20:23:04 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 ) 2020-04-15T20:23:04 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 ) 2020-04-15T20:25:59 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 : 15,684,458 reads read : 31,368,916 reads written : 31,368,916 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: 00:22:12 15684458 reads; of these: 15684458 (100.00%) were paired; of these: 3771230 (24.04%) aligned concordantly 0 times 9758930 (62.22%) aligned concordantly exactly 1 time 2154298 (13.74%) aligned concordantly >1 times ---- 3771230 pairs aligned concordantly 0 times; of these: 240263 (6.37%) aligned discordantly 1 time ---- 3530967 pairs aligned 0 times concordantly or discordantly; of these: 7061934 mates make up the pairs; of these: 6518058 (92.30%) aligned 0 times 283266 (4.01%) aligned exactly 1 time 260610 (3.69%) aligned >1 times 79.22% overall alignment rate Time searching: 00:22:12 Overall time: 00:22:12 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 12 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] 628911 / 12146436 = 0.0518 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 06:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.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 06:00:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:00:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:00:56: 1000000 INFO @ Thu, 16 Apr 2020 06:01:01: 2000000 INFO @ Thu, 16 Apr 2020 06:01:07: 3000000 INFO @ Thu, 16 Apr 2020 06:01:13: 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 @ Thu, 16 Apr 2020 06:01:19: 5000000 INFO @ Thu, 16 Apr 2020 06:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.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 06:01:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:01:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:01:25: 6000000 INFO @ Thu, 16 Apr 2020 06:01:27: 1000000 INFO @ Thu, 16 Apr 2020 06:01:32: 7000000 INFO @ Thu, 16 Apr 2020 06:01:34: 2000000 INFO @ Thu, 16 Apr 2020 06:01:39: 8000000 INFO @ Thu, 16 Apr 2020 06:01:41: 3000000 INFO @ Thu, 16 Apr 2020 06:01:46: 9000000 BedGraph に変換中... INFO @ Thu, 16 Apr 2020 06:01:48: 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 @ Thu, 16 Apr 2020 06:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.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 06:01:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:01:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:01:53: 10000000 INFO @ Thu, 16 Apr 2020 06:01:55: 5000000 INFO @ Thu, 16 Apr 2020 06:01:58: 1000000 INFO @ Thu, 16 Apr 2020 06:02:01: 11000000 INFO @ Thu, 16 Apr 2020 06:02:03: 6000000 INFO @ Thu, 16 Apr 2020 06:02:07: 2000000 INFO @ Thu, 16 Apr 2020 06:02:08: 12000000 INFO @ Thu, 16 Apr 2020 06:02:11: 7000000 INFO @ Thu, 16 Apr 2020 06:02:16: 3000000 INFO @ Thu, 16 Apr 2020 06:02:16: 13000000 INFO @ Thu, 16 Apr 2020 06:02:18: 8000000 INFO @ Thu, 16 Apr 2020 06:02:24: 14000000 INFO @ Thu, 16 Apr 2020 06:02:24: 4000000 INFO @ Thu, 16 Apr 2020 06:02:26: 9000000 INFO @ Thu, 16 Apr 2020 06:02:31: 15000000 INFO @ Thu, 16 Apr 2020 06:02:33: 5000000 INFO @ Thu, 16 Apr 2020 06:02:34: 10000000 INFO @ Thu, 16 Apr 2020 06:02:39: 16000000 INFO @ Thu, 16 Apr 2020 06:02:41: 6000000 INFO @ Thu, 16 Apr 2020 06:02:41: 11000000 INFO @ Thu, 16 Apr 2020 06:02:47: 17000000 INFO @ Thu, 16 Apr 2020 06:02:49: 12000000 INFO @ Thu, 16 Apr 2020 06:02:50: 7000000 INFO @ Thu, 16 Apr 2020 06:02:54: 18000000 INFO @ Thu, 16 Apr 2020 06:02:57: 13000000 INFO @ Thu, 16 Apr 2020 06:02:59: 8000000 INFO @ Thu, 16 Apr 2020 06:03:02: 19000000 INFO @ Thu, 16 Apr 2020 06:03:04: 14000000 INFO @ Thu, 16 Apr 2020 06:03:07: 9000000 INFO @ Thu, 16 Apr 2020 06:03:10: 20000000 INFO @ Thu, 16 Apr 2020 06:03:12: 15000000 INFO @ Thu, 16 Apr 2020 06:03:16: 10000000 INFO @ Thu, 16 Apr 2020 06:03:17: 21000000 INFO @ Thu, 16 Apr 2020 06:03:20: 16000000 INFO @ Thu, 16 Apr 2020 06:03:24: 11000000 INFO @ Thu, 16 Apr 2020 06:03:25: 22000000 INFO @ Thu, 16 Apr 2020 06:03:27: 17000000 INFO @ Thu, 16 Apr 2020 06:03:33: 23000000 INFO @ Thu, 16 Apr 2020 06:03:33: 12000000 INFO @ Thu, 16 Apr 2020 06:03:35: 18000000 INFO @ Thu, 16 Apr 2020 06:03:37: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:03:37: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:03:37: #1 total tags in treatment: 11291866 INFO @ Thu, 16 Apr 2020 06:03:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:03:37: #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 06:03:37: #1 tags after filtering in treatment: 9855494 INFO @ Thu, 16 Apr 2020 06:03:37: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 16 Apr 2020 06:03:37: #1 finished! INFO @ Thu, 16 Apr 2020 06:03:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:03:38: #2 number of paired peaks: 3707 INFO @ Thu, 16 Apr 2020 06:03:38: start model_add_line... INFO @ Thu, 16 Apr 2020 06:03:38: start X-correlation... INFO @ Thu, 16 Apr 2020 06:03:38: end of X-cor INFO @ Thu, 16 Apr 2020 06:03:38: #2 finished! INFO @ Thu, 16 Apr 2020 06:03:38: #2 predicted fragment length is 172 bps INFO @ Thu, 16 Apr 2020 06:03:38: #2 alternative fragment length(s) may be 172 bps INFO @ Thu, 16 Apr 2020 06:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.05_model.r INFO @ Thu, 16 Apr 2020 06:03:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:03:42: 13000000 INFO @ Thu, 16 Apr 2020 06:03:43: 19000000 INFO @ Thu, 16 Apr 2020 06:03:50: 14000000 INFO @ Thu, 16 Apr 2020 06:03:50: 20000000 INFO @ Thu, 16 Apr 2020 06:03:58: 21000000 INFO @ Thu, 16 Apr 2020 06:03:59: 15000000 INFO @ Thu, 16 Apr 2020 06:04:05: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:04:06: 22000000 INFO @ Thu, 16 Apr 2020 06:04:07: 16000000 INFO @ Thu, 16 Apr 2020 06:04:13: 23000000 INFO @ Thu, 16 Apr 2020 06:04:16: 17000000 INFO @ Thu, 16 Apr 2020 06:04:18: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:04:18: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:04:18: #1 total tags in treatment: 11291866 INFO @ Thu, 16 Apr 2020 06:04:18: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:04:18: #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 06:04:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:04:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:04:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.05_summits.bed INFO @ Thu, 16 Apr 2020 06:04:18: Done! INFO @ Thu, 16 Apr 2020 06:04:18: #1 tags after filtering in treatment: 9855494 INFO @ Thu, 16 Apr 2020 06:04:18: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 16 Apr 2020 06:04:18: #1 finished! INFO @ Thu, 16 Apr 2020 06:04:18: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:04:18: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8624 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:04:19: #2 number of paired peaks: 3707 INFO @ Thu, 16 Apr 2020 06:04:19: start model_add_line... INFO @ Thu, 16 Apr 2020 06:04:19: start X-correlation... INFO @ Thu, 16 Apr 2020 06:04:19: end of X-cor INFO @ Thu, 16 Apr 2020 06:04:19: #2 finished! INFO @ Thu, 16 Apr 2020 06:04:19: #2 predicted fragment length is 172 bps INFO @ Thu, 16 Apr 2020 06:04:19: #2 alternative fragment length(s) may be 172 bps INFO @ Thu, 16 Apr 2020 06:04:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.10_model.r INFO @ Thu, 16 Apr 2020 06:04:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:04:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:04:24: 18000000 INFO @ Thu, 16 Apr 2020 06:04:32: 19000000 INFO @ Thu, 16 Apr 2020 06:04:39: 20000000 INFO @ Thu, 16 Apr 2020 06:04:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:04:47: 21000000 INFO @ Thu, 16 Apr 2020 06:04:55: 22000000 INFO @ Thu, 16 Apr 2020 06:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.10_summits.bed INFO @ Thu, 16 Apr 2020 06:04:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6411 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:05:02: 23000000 INFO @ Thu, 16 Apr 2020 06:05:07: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 06:05:07: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 06:05:07: #1 total tags in treatment: 11291866 INFO @ Thu, 16 Apr 2020 06:05:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:05:07: #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 06:05:07: #1 tags after filtering in treatment: 9855494 INFO @ Thu, 16 Apr 2020 06:05:07: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 16 Apr 2020 06:05:07: #1 finished! INFO @ Thu, 16 Apr 2020 06:05:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:05:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:05:08: #2 number of paired peaks: 3707 INFO @ Thu, 16 Apr 2020 06:05:08: start model_add_line... INFO @ Thu, 16 Apr 2020 06:05:08: start X-correlation... INFO @ Thu, 16 Apr 2020 06:05:08: end of X-cor INFO @ Thu, 16 Apr 2020 06:05:08: #2 finished! INFO @ Thu, 16 Apr 2020 06:05:08: #2 predicted fragment length is 172 bps INFO @ Thu, 16 Apr 2020 06:05:08: #2 alternative fragment length(s) may be 172 bps INFO @ Thu, 16 Apr 2020 06:05:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.20_model.r INFO @ Thu, 16 Apr 2020 06:05:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:05:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 06:05:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:05:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:05:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:05:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708291/SRX6708291.20_summits.bed INFO @ Thu, 16 Apr 2020 06:05:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4471 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。