Job ID = 5721049 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T18:56:17 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 ) 2020-04-15T19:04:57 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 ) 2020-04-15T19:04:57 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 ) 2020-04-15T19:04:57 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 ) 2020-04-15T19:45:25 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 ) 2020-04-15T19:47:07 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 ) 2020-04-15T19:53:09 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 : 30,655,412 reads read : 61,310,824 reads written : 61,310,824 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: 01:26:05 30655412 reads; of these: 30655412 (100.00%) were paired; of these: 5307590 (17.31%) aligned concordantly 0 times 20459656 (66.74%) aligned concordantly exactly 1 time 4888166 (15.95%) aligned concordantly >1 times ---- 5307590 pairs aligned concordantly 0 times; of these: 1633370 (30.77%) aligned discordantly 1 time ---- 3674220 pairs aligned 0 times concordantly or discordantly; of these: 7348440 mates make up the pairs; of these: 5417658 (73.73%) aligned 0 times 937694 (12.76%) aligned exactly 1 time 993088 (13.51%) aligned >1 times 91.16% overall alignment rate Time searching: 01:26:06 Overall time: 01:26:06 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 44 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] 10958904 / 26919043 = 0.4071 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 06:43:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.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 06:43:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:43:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:43:54: 1000000 INFO @ Thu, 16 Apr 2020 06:44:01: 2000000 INFO @ Thu, 16 Apr 2020 06:44:07: 3000000 INFO @ Thu, 16 Apr 2020 06:44:14: 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 06:44:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.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 06:44:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:44:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:44:21: 5000000 INFO @ Thu, 16 Apr 2020 06:44:26: 1000000 INFO @ Thu, 16 Apr 2020 06:44:28: 6000000 INFO @ Thu, 16 Apr 2020 06:44:34: 2000000 INFO @ Thu, 16 Apr 2020 06:44:35: 7000000 INFO @ Thu, 16 Apr 2020 06:44:42: 3000000 INFO @ Thu, 16 Apr 2020 06:44:42: 8000000 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 06:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.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 06:44:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:44:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:44:49: 9000000 INFO @ Thu, 16 Apr 2020 06:44:50: 4000000 INFO @ Thu, 16 Apr 2020 06:44:56: 1000000 INFO @ Thu, 16 Apr 2020 06:44:56: 10000000 INFO @ Thu, 16 Apr 2020 06:44:59: 5000000 INFO @ Thu, 16 Apr 2020 06:45:03: 11000000 INFO @ Thu, 16 Apr 2020 06:45:05: 2000000 INFO @ Thu, 16 Apr 2020 06:45:08: 6000000 INFO @ Thu, 16 Apr 2020 06:45:10: 12000000 INFO @ Thu, 16 Apr 2020 06:45:14: 3000000 INFO @ Thu, 16 Apr 2020 06:45:16: 7000000 INFO @ Thu, 16 Apr 2020 06:45:17: 13000000 INFO @ Thu, 16 Apr 2020 06:45:23: 4000000 INFO @ Thu, 16 Apr 2020 06:45:24: 14000000 INFO @ Thu, 16 Apr 2020 06:45:25: 8000000 INFO @ Thu, 16 Apr 2020 06:45:31: 15000000 INFO @ Thu, 16 Apr 2020 06:45:32: 5000000 INFO @ Thu, 16 Apr 2020 06:45:34: 9000000 INFO @ Thu, 16 Apr 2020 06:45:38: 16000000 INFO @ Thu, 16 Apr 2020 06:45:40: 6000000 INFO @ Thu, 16 Apr 2020 06:45:42: 10000000 INFO @ Thu, 16 Apr 2020 06:45:45: 17000000 INFO @ Thu, 16 Apr 2020 06:45:48: 7000000 INFO @ Thu, 16 Apr 2020 06:45:51: 11000000 INFO @ Thu, 16 Apr 2020 06:45:52: 18000000 INFO @ Thu, 16 Apr 2020 06:45:56: 8000000 INFO @ Thu, 16 Apr 2020 06:45:59: 19000000 INFO @ Thu, 16 Apr 2020 06:45:59: 12000000 INFO @ Thu, 16 Apr 2020 06:46:04: 9000000 INFO @ Thu, 16 Apr 2020 06:46:05: 20000000 INFO @ Thu, 16 Apr 2020 06:46:07: 13000000 INFO @ Thu, 16 Apr 2020 06:46:12: 10000000 INFO @ Thu, 16 Apr 2020 06:46:12: 21000000 INFO @ Thu, 16 Apr 2020 06:46:15: 14000000 INFO @ Thu, 16 Apr 2020 06:46:19: 22000000 INFO @ Thu, 16 Apr 2020 06:46:20: 11000000 INFO @ Thu, 16 Apr 2020 06:46:24: 15000000 INFO @ Thu, 16 Apr 2020 06:46:26: 23000000 INFO @ Thu, 16 Apr 2020 06:46:28: 12000000 INFO @ Thu, 16 Apr 2020 06:46:32: 16000000 INFO @ Thu, 16 Apr 2020 06:46:33: 24000000 INFO @ Thu, 16 Apr 2020 06:46:36: 13000000 INFO @ Thu, 16 Apr 2020 06:46:40: 17000000 INFO @ Thu, 16 Apr 2020 06:46:40: 25000000 INFO @ Thu, 16 Apr 2020 06:46:44: 14000000 INFO @ Thu, 16 Apr 2020 06:46:48: 26000000 INFO @ Thu, 16 Apr 2020 06:46:48: 18000000 INFO @ Thu, 16 Apr 2020 06:46:52: 15000000 INFO @ Thu, 16 Apr 2020 06:46:55: 27000000 INFO @ Thu, 16 Apr 2020 06:46:56: 19000000 INFO @ Thu, 16 Apr 2020 06:47:01: 16000000 INFO @ Thu, 16 Apr 2020 06:47:02: 28000000 INFO @ Thu, 16 Apr 2020 06:47:04: 20000000 INFO @ Thu, 16 Apr 2020 06:47:08: 17000000 INFO @ Thu, 16 Apr 2020 06:47:09: 29000000 INFO @ Thu, 16 Apr 2020 06:47:12: 21000000 INFO @ Thu, 16 Apr 2020 06:47:16: 30000000 INFO @ Thu, 16 Apr 2020 06:47:16: 18000000 INFO @ Thu, 16 Apr 2020 06:47:20: 22000000 INFO @ Thu, 16 Apr 2020 06:47:23: 31000000 INFO @ Thu, 16 Apr 2020 06:47:24: 19000000 INFO @ Thu, 16 Apr 2020 06:47:28: 23000000 INFO @ Thu, 16 Apr 2020 06:47:30: 32000000 INFO @ Thu, 16 Apr 2020 06:47:32: 20000000 INFO @ Thu, 16 Apr 2020 06:47:37: 33000000 INFO @ Thu, 16 Apr 2020 06:47:37: 24000000 INFO @ Thu, 16 Apr 2020 06:47:41: 21000000 INFO @ Thu, 16 Apr 2020 06:47:43: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:47:43: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:47:43: #1 total tags in treatment: 14760902 INFO @ Thu, 16 Apr 2020 06:47:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:47:43: #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 06:47:44: #1 tags after filtering in treatment: 12912410 INFO @ Thu, 16 Apr 2020 06:47:44: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 16 Apr 2020 06:47:44: #1 finished! INFO @ Thu, 16 Apr 2020 06:47:44: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:47:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:47:45: #2 number of paired peaks: 2867 INFO @ Thu, 16 Apr 2020 06:47:45: start model_add_line... INFO @ Thu, 16 Apr 2020 06:47:45: start X-correlation... INFO @ Thu, 16 Apr 2020 06:47:45: end of X-cor INFO @ Thu, 16 Apr 2020 06:47:45: #2 finished! INFO @ Thu, 16 Apr 2020 06:47:45: #2 predicted fragment length is 238 bps INFO @ Thu, 16 Apr 2020 06:47:45: #2 alternative fragment length(s) may be 238 bps INFO @ Thu, 16 Apr 2020 06:47:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.05_model.r WARNING @ Thu, 16 Apr 2020 06:47:45: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:47:45: #2 You may need to consider one of the other alternative d(s): 238 WARNING @ Thu, 16 Apr 2020 06:47:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:47:45: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:47:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:47:45: 25000000 INFO @ Thu, 16 Apr 2020 06:47:49: 22000000 INFO @ Thu, 16 Apr 2020 06:47:53: 26000000 INFO @ Thu, 16 Apr 2020 06:47:57: 23000000 INFO @ Thu, 16 Apr 2020 06:48:02: 27000000 INFO @ Thu, 16 Apr 2020 06:48:05: 24000000 INFO @ Thu, 16 Apr 2020 06:48:10: 28000000 INFO @ Thu, 16 Apr 2020 06:48:14: 25000000 INFO @ Thu, 16 Apr 2020 06:48:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:48:18: 29000000 INFO @ Thu, 16 Apr 2020 06:48:23: 26000000 INFO @ Thu, 16 Apr 2020 06:48:26: 30000000 INFO @ Thu, 16 Apr 2020 06:48:31: 27000000 INFO @ Thu, 16 Apr 2020 06:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.05_summits.bed INFO @ Thu, 16 Apr 2020 06:48:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12827 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:48:34: 31000000 INFO @ Thu, 16 Apr 2020 06:48:40: 28000000 INFO @ Thu, 16 Apr 2020 06:48:43: 32000000 INFO @ Thu, 16 Apr 2020 06:48:48: 29000000 INFO @ Thu, 16 Apr 2020 06:48:51: 33000000 INFO @ Thu, 16 Apr 2020 06:48:56: 30000000 INFO @ Thu, 16 Apr 2020 06:48:59: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:48:59: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:48:59: #1 total tags in treatment: 14760902 INFO @ Thu, 16 Apr 2020 06:48:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:48:59: #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 06:48:59: #1 tags after filtering in treatment: 12912410 INFO @ Thu, 16 Apr 2020 06:48:59: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 16 Apr 2020 06:48:59: #1 finished! INFO @ Thu, 16 Apr 2020 06:48:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:49:00: #2 number of paired peaks: 2867 INFO @ Thu, 16 Apr 2020 06:49:00: start model_add_line... INFO @ Thu, 16 Apr 2020 06:49:00: start X-correlation... INFO @ Thu, 16 Apr 2020 06:49:00: end of X-cor INFO @ Thu, 16 Apr 2020 06:49:00: #2 finished! INFO @ Thu, 16 Apr 2020 06:49:00: #2 predicted fragment length is 238 bps INFO @ Thu, 16 Apr 2020 06:49:00: #2 alternative fragment length(s) may be 238 bps INFO @ Thu, 16 Apr 2020 06:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.10_model.r WARNING @ Thu, 16 Apr 2020 06:49:00: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:49:00: #2 You may need to consider one of the other alternative d(s): 238 WARNING @ Thu, 16 Apr 2020 06:49:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:49:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:49:04: 31000000 INFO @ Thu, 16 Apr 2020 06:49:12: 32000000 INFO @ Thu, 16 Apr 2020 06:49:20: 33000000 INFO @ Thu, 16 Apr 2020 06:49:27: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:49:27: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:49:27: #1 total tags in treatment: 14760902 INFO @ Thu, 16 Apr 2020 06:49:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:49:27: #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 06:49:28: #1 tags after filtering in treatment: 12912410 INFO @ Thu, 16 Apr 2020 06:49:28: #1 Redundant rate of treatment: 0.13 INFO @ Thu, 16 Apr 2020 06:49:28: #1 finished! INFO @ Thu, 16 Apr 2020 06:49:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:49:29: #2 number of paired peaks: 2867 INFO @ Thu, 16 Apr 2020 06:49:29: start model_add_line... INFO @ Thu, 16 Apr 2020 06:49:29: start X-correlation... INFO @ Thu, 16 Apr 2020 06:49:29: end of X-cor INFO @ Thu, 16 Apr 2020 06:49:29: #2 finished! INFO @ Thu, 16 Apr 2020 06:49:29: #2 predicted fragment length is 238 bps INFO @ Thu, 16 Apr 2020 06:49:29: #2 alternative fragment length(s) may be 238 bps INFO @ Thu, 16 Apr 2020 06:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.20_model.r WARNING @ Thu, 16 Apr 2020 06:49:29: #2 Since the d (238) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:49:29: #2 You may need to consider one of the other alternative d(s): 238 WARNING @ Thu, 16 Apr 2020 06:49:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:49:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:49:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:49:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:49:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:49:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.10_summits.bed INFO @ Thu, 16 Apr 2020 06:49:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9478 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:50:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386782/SRX6386782.20_summits.bed INFO @ Thu, 16 Apr 2020 06:50:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5863 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。