Job ID = 5720971 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:06:40 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 : 21,855,111 reads read : 43,710,222 reads written : 43,710,222 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: 00:38:09 21855111 reads; of these: 21855111 (100.00%) were paired; of these: 13483695 (61.70%) aligned concordantly 0 times 6920511 (31.67%) aligned concordantly exactly 1 time 1450905 (6.64%) aligned concordantly >1 times ---- 13483695 pairs aligned concordantly 0 times; of these: 867219 (6.43%) aligned discordantly 1 time ---- 12616476 pairs aligned 0 times concordantly or discordantly; of these: 25232952 mates make up the pairs; of these: 23005975 (91.17%) aligned 0 times 1524842 (6.04%) aligned exactly 1 time 702135 (2.78%) aligned >1 times 47.37% overall alignment rate Time searching: 00:38:09 Overall time: 00:38:09 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 16 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] 7412581 / 9198068 = 0.8059 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 05:02:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.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 05:02:59: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:02:59: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:03:07: 1000000 INFO @ Thu, 16 Apr 2020 05:03:16: 2000000 INFO @ Thu, 16 Apr 2020 05:03:24: 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 05:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.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 05:03:29: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:03:29: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:03:33: 4000000 INFO @ Thu, 16 Apr 2020 05:03:39: 1000000 INFO @ Thu, 16 Apr 2020 05:03:42: 5000000 INFO @ Thu, 16 Apr 2020 05:03:48: 2000000 INFO @ Thu, 16 Apr 2020 05:03:51: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 05:03:51: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 05:03:51: #1 total tags in treatment: 1580771 INFO @ Thu, 16 Apr 2020 05:03:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:03:51: #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 05:03:51: #1 tags after filtering in treatment: 1343147 INFO @ Thu, 16 Apr 2020 05:03:51: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:03:51: #1 finished! INFO @ Thu, 16 Apr 2020 05:03:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:03:51: #2 number of paired peaks: 1641 INFO @ Thu, 16 Apr 2020 05:03:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:03:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:03:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:03:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:03:51: #2 predicted fragment length is 178 bps INFO @ Thu, 16 Apr 2020 05:03:51: #2 alternative fragment length(s) may be 178 bps INFO @ Thu, 16 Apr 2020 05:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.05_model.r WARNING @ Thu, 16 Apr 2020 05:03:51: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:03:51: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Thu, 16 Apr 2020 05:03:51: #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 05:03:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:03:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:03:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:03:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:03:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.05_summits.bed INFO @ Thu, 16 Apr 2020 05:03:56: Done! 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 05:03:57: 3000000 INFO @ Thu, 16 Apr 2020 05:04:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.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 05:04:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:04:00: #1 read treatment tags... pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2278 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:04:07: 4000000 INFO @ Thu, 16 Apr 2020 05:04:10: 1000000 INFO @ Thu, 16 Apr 2020 05:04:17: 5000000 INFO @ Thu, 16 Apr 2020 05:04:19: 2000000 INFO @ Thu, 16 Apr 2020 05:04:25: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 05:04:25: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 05:04:25: #1 total tags in treatment: 1580771 INFO @ Thu, 16 Apr 2020 05:04:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:04:25: #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 05:04:25: #1 tags after filtering in treatment: 1343147 INFO @ Thu, 16 Apr 2020 05:04:25: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:04:25: #1 finished! INFO @ Thu, 16 Apr 2020 05:04:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:04:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:04:25: #2 number of paired peaks: 1641 INFO @ Thu, 16 Apr 2020 05:04:25: start model_add_line... INFO @ Thu, 16 Apr 2020 05:04:25: start X-correlation... INFO @ Thu, 16 Apr 2020 05:04:25: end of X-cor INFO @ Thu, 16 Apr 2020 05:04:25: #2 finished! INFO @ Thu, 16 Apr 2020 05:04:25: #2 predicted fragment length is 178 bps INFO @ Thu, 16 Apr 2020 05:04:25: #2 alternative fragment length(s) may be 178 bps INFO @ Thu, 16 Apr 2020 05:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.10_model.r WARNING @ Thu, 16 Apr 2020 05:04:25: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:04:25: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Thu, 16 Apr 2020 05:04:25: #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 05:04:25: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:04:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:04:28: 3000000 INFO @ Thu, 16 Apr 2020 05:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.10_summits.bed INFO @ Thu, 16 Apr 2020 05:04:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1067 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:04:37: 4000000 INFO @ Thu, 16 Apr 2020 05:04:46: 5000000 INFO @ Thu, 16 Apr 2020 05:04:54: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 05:04:54: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 05:04:54: #1 total tags in treatment: 1580771 INFO @ Thu, 16 Apr 2020 05:04:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:04:54: #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 05:04:54: #1 tags after filtering in treatment: 1343147 INFO @ Thu, 16 Apr 2020 05:04:54: #1 Redundant rate of treatment: 0.15 INFO @ Thu, 16 Apr 2020 05:04:54: #1 finished! INFO @ Thu, 16 Apr 2020 05:04:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:04:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:04:54: #2 number of paired peaks: 1641 INFO @ Thu, 16 Apr 2020 05:04:54: start model_add_line... INFO @ Thu, 16 Apr 2020 05:04:54: start X-correlation... INFO @ Thu, 16 Apr 2020 05:04:54: end of X-cor INFO @ Thu, 16 Apr 2020 05:04:54: #2 finished! INFO @ Thu, 16 Apr 2020 05:04:54: #2 predicted fragment length is 178 bps INFO @ Thu, 16 Apr 2020 05:04:54: #2 alternative fragment length(s) may be 178 bps INFO @ Thu, 16 Apr 2020 05:04:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.20_model.r WARNING @ Thu, 16 Apr 2020 05:04:54: #2 Since the d (178) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:04:54: #2 You may need to consider one of the other alternative d(s): 178 WARNING @ Thu, 16 Apr 2020 05:04:54: #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 05:04:54: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:04:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:04:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386763/SRX6386763.20_summits.bed INFO @ Thu, 16 Apr 2020 05:04:59: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (556 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。