Job ID = 5721053 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:19:30 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 ) 2020-04-15T19:43:18 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 ) spots read : 34,482,624 reads read : 68,965,248 reads written : 68,965,248 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: 00:57:03 34482624 reads; of these: 34482624 (100.00%) were paired; of these: 21018386 (60.95%) aligned concordantly 0 times 9918204 (28.76%) aligned concordantly exactly 1 time 3546034 (10.28%) aligned concordantly >1 times ---- 21018386 pairs aligned concordantly 0 times; of these: 1351077 (6.43%) aligned discordantly 1 time ---- 19667309 pairs aligned 0 times concordantly or discordantly; of these: 39334618 mates make up the pairs; of these: 37690135 (95.82%) aligned 0 times 509039 (1.29%) aligned exactly 1 time 1135444 (2.89%) aligned >1 times 45.35% overall alignment rate Time searching: 00:57:04 Overall time: 00:57:04 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 24 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] 12311064 / 14731847 = 0.8357 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 06:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.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 06:06:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:06:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:06:10: 1000000 INFO @ Thu, 16 Apr 2020 06:06:21: 2000000 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 06:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.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 06:06:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:06:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:06:32: 3000000 INFO @ Thu, 16 Apr 2020 06:06:41: 1000000 INFO @ Thu, 16 Apr 2020 06:06:44: 4000000 INFO @ Thu, 16 Apr 2020 06:06:51: 2000000 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 06:06:57: 5000000 INFO @ Thu, 16 Apr 2020 06:07:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.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 06:07:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:07:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:07:02: 3000000 INFO @ Thu, 16 Apr 2020 06:07:09: 6000000 INFO @ Thu, 16 Apr 2020 06:07:11: 1000000 INFO @ Thu, 16 Apr 2020 06:07:13: 4000000 INFO @ Thu, 16 Apr 2020 06:07:17: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:07:17: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:07:17: #1 total tags in treatment: 2023265 INFO @ Thu, 16 Apr 2020 06:07:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:07:17: #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 06:07:17: #1 tags after filtering in treatment: 1832027 INFO @ Thu, 16 Apr 2020 06:07:17: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 06:07:17: #1 finished! INFO @ Thu, 16 Apr 2020 06:07:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:07:18: #2 number of paired peaks: 4828 INFO @ Thu, 16 Apr 2020 06:07:18: start model_add_line... INFO @ Thu, 16 Apr 2020 06:07:18: start X-correlation... INFO @ Thu, 16 Apr 2020 06:07:18: end of X-cor INFO @ Thu, 16 Apr 2020 06:07:18: #2 finished! INFO @ Thu, 16 Apr 2020 06:07:18: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 06:07:18: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 06:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.05_model.r WARNING @ Thu, 16 Apr 2020 06:07:18: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:07:18: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 16 Apr 2020 06:07:18: #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 06:07:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:07:22: 2000000 INFO @ Thu, 16 Apr 2020 06:07:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:07:23: 5000000 INFO @ Thu, 16 Apr 2020 06:07:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:07:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:07:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.05_summits.bed INFO @ Thu, 16 Apr 2020 06:07:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4282 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:07:33: 3000000 INFO @ Thu, 16 Apr 2020 06:07:34: 6000000 INFO @ Thu, 16 Apr 2020 06:07:40: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:07:40: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:07:40: #1 total tags in treatment: 2023265 INFO @ Thu, 16 Apr 2020 06:07:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:07:40: #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 06:07:40: #1 tags after filtering in treatment: 1832027 INFO @ Thu, 16 Apr 2020 06:07:40: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 06:07:40: #1 finished! INFO @ Thu, 16 Apr 2020 06:07:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:07:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:07:41: #2 number of paired peaks: 4828 INFO @ Thu, 16 Apr 2020 06:07:41: start model_add_line... INFO @ Thu, 16 Apr 2020 06:07:41: start X-correlation... INFO @ Thu, 16 Apr 2020 06:07:41: end of X-cor INFO @ Thu, 16 Apr 2020 06:07:41: #2 finished! INFO @ Thu, 16 Apr 2020 06:07:41: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 06:07:41: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 06:07:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.10_model.r WARNING @ Thu, 16 Apr 2020 06:07:41: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:07:41: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 16 Apr 2020 06:07:41: #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 06:07:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:07:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:07:43: 4000000 INFO @ Thu, 16 Apr 2020 06:07:45: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.10_summits.bed INFO @ Thu, 16 Apr 2020 06:07:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2714 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:07:52: 5000000 INFO @ Thu, 16 Apr 2020 06:08:02: 6000000 INFO @ Thu, 16 Apr 2020 06:08:07: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:08:07: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:08:07: #1 total tags in treatment: 2023265 INFO @ Thu, 16 Apr 2020 06:08:07: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:08:07: #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 06:08:07: #1 tags after filtering in treatment: 1832027 INFO @ Thu, 16 Apr 2020 06:08:07: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 06:08:07: #1 finished! INFO @ Thu, 16 Apr 2020 06:08:07: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:08:08: #2 number of paired peaks: 4828 INFO @ Thu, 16 Apr 2020 06:08:08: start model_add_line... INFO @ Thu, 16 Apr 2020 06:08:08: start X-correlation... INFO @ Thu, 16 Apr 2020 06:08:08: end of X-cor INFO @ Thu, 16 Apr 2020 06:08:08: #2 finished! INFO @ Thu, 16 Apr 2020 06:08:08: #2 predicted fragment length is 217 bps INFO @ Thu, 16 Apr 2020 06:08:08: #2 alternative fragment length(s) may be 217 bps INFO @ Thu, 16 Apr 2020 06:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.20_model.r WARNING @ Thu, 16 Apr 2020 06:08:08: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:08:08: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Thu, 16 Apr 2020 06:08:08: #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 06:08:08: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:08:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 06:08:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:08:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:08:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386785/SRX6386785.20_summits.bed INFO @ Thu, 16 Apr 2020 06:08:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1323 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。