Job ID = 5721071 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:03:11 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 ) 2020-04-15T19:10:35 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 ) 2020-04-15T19:24:47 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 ) 2020-04-15T19:24:47 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 : 13,636,505 reads read : 27,273,010 reads written : 27,273,010 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: 01:16:36 13636505 reads; of these: 13636505 (100.00%) were paired; of these: 3692299 (27.08%) aligned concordantly 0 times 4589005 (33.65%) aligned concordantly exactly 1 time 5355201 (39.27%) aligned concordantly >1 times ---- 3692299 pairs aligned concordantly 0 times; of these: 1123599 (30.43%) aligned discordantly 1 time ---- 2568700 pairs aligned 0 times concordantly or discordantly; of these: 5137400 mates make up the pairs; of these: 2398821 (46.69%) aligned 0 times 1139651 (22.18%) aligned exactly 1 time 1598928 (31.12%) aligned >1 times 91.20% overall alignment rate Time searching: 01:16:36 Overall time: 01:16:36 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] 3487866 / 10729892 = 0.3251 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 05:53:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.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 05:53:14: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:53:14: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:53:22: 1000000 INFO @ Thu, 16 Apr 2020 05:53:30: 2000000 INFO @ Thu, 16 Apr 2020 05:53:39: 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 05:53:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.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 05:53:43: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:53:43: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:53:48: 4000000 INFO @ Thu, 16 Apr 2020 05:53:52: 1000000 INFO @ Thu, 16 Apr 2020 05:53:58: 5000000 INFO @ Thu, 16 Apr 2020 05:54:02: 2000000 INFO @ Thu, 16 Apr 2020 05:54:07: 6000000 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 05:54:12: 3000000 INFO @ Thu, 16 Apr 2020 05:54:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.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 05:54:13: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:54:13: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:54:17: 7000000 INFO @ Thu, 16 Apr 2020 05:54:22: 4000000 INFO @ Thu, 16 Apr 2020 05:54:22: 1000000 INFO @ Thu, 16 Apr 2020 05:54:27: 8000000 INFO @ Thu, 16 Apr 2020 05:54:31: 5000000 INFO @ Thu, 16 Apr 2020 05:54:32: 2000000 INFO @ Thu, 16 Apr 2020 05:54:37: 9000000 INFO @ Thu, 16 Apr 2020 05:54:41: 6000000 INFO @ Thu, 16 Apr 2020 05:54:42: 3000000 INFO @ Thu, 16 Apr 2020 05:54:46: 10000000 INFO @ Thu, 16 Apr 2020 05:54:51: 7000000 INFO @ Thu, 16 Apr 2020 05:54:52: 4000000 INFO @ Thu, 16 Apr 2020 05:54:56: 11000000 INFO @ Thu, 16 Apr 2020 05:55:01: 8000000 INFO @ Thu, 16 Apr 2020 05:55:02: 5000000 INFO @ Thu, 16 Apr 2020 05:55:06: 12000000 INFO @ Thu, 16 Apr 2020 05:55:10: 9000000 INFO @ Thu, 16 Apr 2020 05:55:11: 6000000 INFO @ Thu, 16 Apr 2020 05:55:16: 13000000 INFO @ Thu, 16 Apr 2020 05:55:20: 10000000 INFO @ Thu, 16 Apr 2020 05:55:21: 7000000 INFO @ Thu, 16 Apr 2020 05:55:26: 14000000 INFO @ Thu, 16 Apr 2020 05:55:30: 11000000 INFO @ Thu, 16 Apr 2020 05:55:31: 8000000 INFO @ Thu, 16 Apr 2020 05:55:36: 15000000 INFO @ Thu, 16 Apr 2020 05:55:40: 12000000 INFO @ Thu, 16 Apr 2020 05:55:41: 9000000 INFO @ Thu, 16 Apr 2020 05:55:46: 16000000 INFO @ Thu, 16 Apr 2020 05:55:50: 13000000 INFO @ Thu, 16 Apr 2020 05:55:50: 10000000 INFO @ Thu, 16 Apr 2020 05:55:55: 17000000 INFO @ Thu, 16 Apr 2020 05:56:00: 14000000 INFO @ Thu, 16 Apr 2020 05:56:00: 11000000 INFO @ Thu, 16 Apr 2020 05:56:04: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:56:04: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:56:04: #1 total tags in treatment: 6534721 INFO @ Thu, 16 Apr 2020 05:56:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:56:04: #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 05:56:04: #1 tags after filtering in treatment: 4662899 INFO @ Thu, 16 Apr 2020 05:56:04: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 16 Apr 2020 05:56:04: #1 finished! INFO @ Thu, 16 Apr 2020 05:56:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:56:05: #2 number of paired peaks: 6725 INFO @ Thu, 16 Apr 2020 05:56:05: start model_add_line... INFO @ Thu, 16 Apr 2020 05:56:05: start X-correlation... INFO @ Thu, 16 Apr 2020 05:56:05: end of X-cor INFO @ Thu, 16 Apr 2020 05:56:05: #2 finished! INFO @ Thu, 16 Apr 2020 05:56:05: #2 predicted fragment length is 247 bps INFO @ Thu, 16 Apr 2020 05:56:05: #2 alternative fragment length(s) may be 247 bps INFO @ Thu, 16 Apr 2020 05:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.05_model.r WARNING @ Thu, 16 Apr 2020 05:56:05: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:56:05: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Thu, 16 Apr 2020 05:56:05: #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 05:56:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:56:10: 15000000 INFO @ Thu, 16 Apr 2020 05:56:10: 12000000 INFO @ Thu, 16 Apr 2020 05:56:19: 16000000 INFO @ Thu, 16 Apr 2020 05:56:20: 13000000 INFO @ Thu, 16 Apr 2020 05:56:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:56:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:56:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.05_summits.bed INFO @ Thu, 16 Apr 2020 05:56:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13484 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:56:29: 17000000 INFO @ Thu, 16 Apr 2020 05:56:30: 14000000 INFO @ Thu, 16 Apr 2020 05:56:37: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:56:37: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:56:37: #1 total tags in treatment: 6534721 INFO @ Thu, 16 Apr 2020 05:56:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:56:37: #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 05:56:37: #1 tags after filtering in treatment: 4662899 INFO @ Thu, 16 Apr 2020 05:56:37: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 16 Apr 2020 05:56:37: #1 finished! INFO @ Thu, 16 Apr 2020 05:56:37: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:56:38: #2 number of paired peaks: 6725 INFO @ Thu, 16 Apr 2020 05:56:38: start model_add_line... INFO @ Thu, 16 Apr 2020 05:56:38: start X-correlation... INFO @ Thu, 16 Apr 2020 05:56:38: end of X-cor INFO @ Thu, 16 Apr 2020 05:56:38: #2 finished! INFO @ Thu, 16 Apr 2020 05:56:38: #2 predicted fragment length is 247 bps INFO @ Thu, 16 Apr 2020 05:56:38: #2 alternative fragment length(s) may be 247 bps INFO @ Thu, 16 Apr 2020 05:56:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.10_model.r WARNING @ Thu, 16 Apr 2020 05:56:38: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:56:38: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Thu, 16 Apr 2020 05:56:38: #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 05:56:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:56:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:56:39: 15000000 INFO @ Thu, 16 Apr 2020 05:56:48: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 05:56:53: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:56:57: 17000000 INFO @ Thu, 16 Apr 2020 05:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.10_summits.bed INFO @ Thu, 16 Apr 2020 05:57:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8896 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:57:05: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 05:57:05: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 05:57:05: #1 total tags in treatment: 6534721 INFO @ Thu, 16 Apr 2020 05:57:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:57:05: #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 05:57:05: #1 tags after filtering in treatment: 4662899 INFO @ Thu, 16 Apr 2020 05:57:05: #1 Redundant rate of treatment: 0.29 INFO @ Thu, 16 Apr 2020 05:57:05: #1 finished! INFO @ Thu, 16 Apr 2020 05:57:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:57:06: #2 number of paired peaks: 6725 INFO @ Thu, 16 Apr 2020 05:57:06: start model_add_line... INFO @ Thu, 16 Apr 2020 05:57:06: start X-correlation... INFO @ Thu, 16 Apr 2020 05:57:06: end of X-cor INFO @ Thu, 16 Apr 2020 05:57:06: #2 finished! INFO @ Thu, 16 Apr 2020 05:57:06: #2 predicted fragment length is 247 bps INFO @ Thu, 16 Apr 2020 05:57:06: #2 alternative fragment length(s) may be 247 bps INFO @ Thu, 16 Apr 2020 05:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.20_model.r WARNING @ Thu, 16 Apr 2020 05:57:06: #2 Since the d (247) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:57:06: #2 You may need to consider one of the other alternative d(s): 247 WARNING @ Thu, 16 Apr 2020 05:57:06: #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 05:57:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:57:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 16 Apr 2020 05:57:21: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:57:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:57:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448069/SRX6448069.20_summits.bed INFO @ Thu, 16 Apr 2020 05:57:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4944 records, 4 fields): 6 millis CompletedMACS2peakCalling