Job ID = 5721170 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,497,093 reads read : 22,994,186 reads written : 22,994,186 spots read : 11,512,021 reads read : 23,024,042 reads written : 23,024,042 2020-04-15T20:41:56 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 ) 2020-04-15T20:41:56 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 : 11,151,966 reads read : 22,303,932 reads written : 22,303,932 2020-04-15T20:52:36 fasterq-dump.2.9.6 sys: error unknown while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 11,271,932 reads read : 22,543,864 reads written : 22,543,864 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: 00:07:29 45433012 reads; of these: 45433012 (100.00%) were paired; of these: 44584984 (98.13%) aligned concordantly 0 times 637931 (1.40%) aligned concordantly exactly 1 time 210097 (0.46%) aligned concordantly >1 times ---- 44584984 pairs aligned concordantly 0 times; of these: 4989 (0.01%) aligned discordantly 1 time ---- 44579995 pairs aligned 0 times concordantly or discordantly; of these: 89159990 mates make up the pairs; of these: 88341456 (99.08%) aligned 0 times 110615 (0.12%) aligned exactly 1 time 707919 (0.79%) aligned >1 times 2.78% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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_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] 26754 / 852063 = 0.0314 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 06:02:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.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 06:02:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:02:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:03:00: 1000000 INFO @ Thu, 16 Apr 2020 06:03:04: 2000000 INFO @ Thu, 16 Apr 2020 06:03:06: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:03:06: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:03:06: #1 total tags in treatment: 821323 INFO @ Thu, 16 Apr 2020 06:03:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:03:06: #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 06:03:06: #1 tags after filtering in treatment: 784115 INFO @ Thu, 16 Apr 2020 06:03:06: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:03:06: #1 finished! INFO @ Thu, 16 Apr 2020 06:03:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:03:06: #2 number of paired peaks: 5332 INFO @ Thu, 16 Apr 2020 06:03:06: start model_add_line... INFO @ Thu, 16 Apr 2020 06:03:06: start X-correlation... INFO @ Thu, 16 Apr 2020 06:03:06: end of X-cor INFO @ Thu, 16 Apr 2020 06:03:06: #2 finished! INFO @ Thu, 16 Apr 2020 06:03:06: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 06:03:06: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 06:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.05_model.r INFO @ Thu, 16 Apr 2020 06:03:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:03:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.05_summits.bed INFO @ Thu, 16 Apr 2020 06:03:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1304 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 06:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.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 06:03:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:03:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:03:31: 1000000 INFO @ Thu, 16 Apr 2020 06:03:35: 2000000 INFO @ Thu, 16 Apr 2020 06:03:37: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:03:37: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:03:37: #1 total tags in treatment: 821323 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: 784115 INFO @ Thu, 16 Apr 2020 06:03:37: #1 Redundant rate of treatment: 0.05 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 06:03:37: #2 number of paired peaks: 5332 INFO @ Thu, 16 Apr 2020 06:03:37: start model_add_line... INFO @ Thu, 16 Apr 2020 06:03:37: start X-correlation... INFO @ Thu, 16 Apr 2020 06:03:37: end of X-cor INFO @ Thu, 16 Apr 2020 06:03:37: #2 finished! INFO @ Thu, 16 Apr 2020 06:03:37: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 06:03:37: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 06:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.10_model.r INFO @ Thu, 16 Apr 2020 06:03:37: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:03:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:03:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:03:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:03:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.10_summits.bed INFO @ Thu, 16 Apr 2020 06:03:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (425 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 06:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.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 06:03:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:03:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:04:01: 1000000 INFO @ Thu, 16 Apr 2020 06:04:06: 2000000 INFO @ Thu, 16 Apr 2020 06:04:09: #1 tag size is determined as 39 bps INFO @ Thu, 16 Apr 2020 06:04:09: #1 tag size = 39 INFO @ Thu, 16 Apr 2020 06:04:09: #1 total tags in treatment: 821323 INFO @ Thu, 16 Apr 2020 06:04:09: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:04:09: #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 06:04:09: #1 tags after filtering in treatment: 784115 INFO @ Thu, 16 Apr 2020 06:04:09: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:04:09: #1 finished! INFO @ Thu, 16 Apr 2020 06:04:09: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:04:09: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:04:09: #2 number of paired peaks: 5332 INFO @ Thu, 16 Apr 2020 06:04:09: start model_add_line... INFO @ Thu, 16 Apr 2020 06:04:09: start X-correlation... INFO @ Thu, 16 Apr 2020 06:04:09: end of X-cor INFO @ Thu, 16 Apr 2020 06:04:09: #2 finished! INFO @ Thu, 16 Apr 2020 06:04:09: #2 predicted fragment length is 199 bps INFO @ Thu, 16 Apr 2020 06:04:09: #2 alternative fragment length(s) may be 199 bps INFO @ Thu, 16 Apr 2020 06:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.20_model.r INFO @ Thu, 16 Apr 2020 06:04:09: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:04:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:04:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6762283/SRX6762283.20_summits.bed INFO @ Thu, 16 Apr 2020 06:04:12: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。