Job ID = 5721068 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T19:00:17 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 ) spots read : 4,572,222 reads read : 9,144,444 reads written : 9,144,444 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: 00:15:59 4572222 reads; of these: 4572222 (100.00%) were paired; of these: 453054 (9.91%) aligned concordantly 0 times 3016616 (65.98%) aligned concordantly exactly 1 time 1102552 (24.11%) aligned concordantly >1 times ---- 453054 pairs aligned concordantly 0 times; of these: 224515 (49.56%) aligned discordantly 1 time ---- 228539 pairs aligned 0 times concordantly or discordantly; of these: 457078 mates make up the pairs; of these: 180524 (39.50%) aligned 0 times 80295 (17.57%) aligned exactly 1 time 196259 (42.94%) aligned >1 times 98.03% overall alignment rate Time searching: 00:15:59 Overall time: 00:15:59 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 8 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] 458408 / 4295542 = 0.1067 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 04:25:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.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 04:25:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:25:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:25:35: 1000000 INFO @ Thu, 16 Apr 2020 04:25:42: 2000000 INFO @ Thu, 16 Apr 2020 04:25:48: 3000000 INFO @ Thu, 16 Apr 2020 04:25:55: 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 04:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.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 04:25:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:25:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:26:03: 5000000 INFO @ Thu, 16 Apr 2020 04:26:07: 1000000 INFO @ Thu, 16 Apr 2020 04:26:11: 6000000 INFO @ Thu, 16 Apr 2020 04:26:16: 2000000 INFO @ Thu, 16 Apr 2020 04:26:19: 7000000 INFO @ Thu, 16 Apr 2020 04:26:24: 3000000 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 04:26:27: 8000000 INFO @ Thu, 16 Apr 2020 04:26:27: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:26:27: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:26:27: #1 total tags in treatment: 3676467 INFO @ Thu, 16 Apr 2020 04:26:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:26:27: #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 04:26:28: #1 tags after filtering in treatment: 3557040 INFO @ Thu, 16 Apr 2020 04:26:28: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:26:28: #1 finished! INFO @ Thu, 16 Apr 2020 04:26:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:26:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:26:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.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 04:26:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:26:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:26:28: #2 number of paired peaks: 1109 INFO @ Thu, 16 Apr 2020 04:26:28: start model_add_line... INFO @ Thu, 16 Apr 2020 04:26:28: start X-correlation... INFO @ Thu, 16 Apr 2020 04:26:28: end of X-cor INFO @ Thu, 16 Apr 2020 04:26:28: #2 finished! INFO @ Thu, 16 Apr 2020 04:26:28: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 04:26:28: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 04:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.05_model.r WARNING @ Thu, 16 Apr 2020 04:26:28: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:26:28: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 04:26:28: #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 04:26:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:26:33: 4000000 INFO @ Thu, 16 Apr 2020 04:26:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:26:36: 1000000 INFO @ Thu, 16 Apr 2020 04:26:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:26:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:26:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.05_summits.bed INFO @ Thu, 16 Apr 2020 04:26:39: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1298 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:26:45: 2000000 INFO @ Thu, 16 Apr 2020 04:26:45: 5000000 INFO @ Thu, 16 Apr 2020 04:26:53: 3000000 INFO @ Thu, 16 Apr 2020 04:26:55: 6000000 INFO @ Thu, 16 Apr 2020 04:27:02: 4000000 INFO @ Thu, 16 Apr 2020 04:27:04: 7000000 INFO @ Thu, 16 Apr 2020 04:27:10: 5000000 INFO @ Thu, 16 Apr 2020 04:27:13: 8000000 INFO @ Thu, 16 Apr 2020 04:27:14: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:27:14: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:27:14: #1 total tags in treatment: 3676467 INFO @ Thu, 16 Apr 2020 04:27:14: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:27:14: #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 04:27:14: #1 tags after filtering in treatment: 3557040 INFO @ Thu, 16 Apr 2020 04:27:14: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:27:14: #1 finished! INFO @ Thu, 16 Apr 2020 04:27:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:27:14: #2 number of paired peaks: 1109 INFO @ Thu, 16 Apr 2020 04:27:14: start model_add_line... INFO @ Thu, 16 Apr 2020 04:27:14: start X-correlation... INFO @ Thu, 16 Apr 2020 04:27:14: end of X-cor INFO @ Thu, 16 Apr 2020 04:27:14: #2 finished! INFO @ Thu, 16 Apr 2020 04:27:14: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 04:27:14: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 04:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.10_model.r WARNING @ Thu, 16 Apr 2020 04:27:14: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:27:14: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 04:27:14: #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 04:27:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:27:18: 6000000 INFO @ Thu, 16 Apr 2020 04:27:22: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:27:25: 7000000 INFO @ Thu, 16 Apr 2020 04:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.10_summits.bed INFO @ Thu, 16 Apr 2020 04:27:26: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (761 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:27:33: 8000000 INFO @ Thu, 16 Apr 2020 04:27:33: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:27:33: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:27:33: #1 total tags in treatment: 3676467 INFO @ Thu, 16 Apr 2020 04:27:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:27:33: #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 04:27:33: #1 tags after filtering in treatment: 3557040 INFO @ Thu, 16 Apr 2020 04:27:33: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:27:33: #1 finished! INFO @ Thu, 16 Apr 2020 04:27:33: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:27:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:27:34: #2 number of paired peaks: 1109 INFO @ Thu, 16 Apr 2020 04:27:34: start model_add_line... INFO @ Thu, 16 Apr 2020 04:27:34: start X-correlation... INFO @ Thu, 16 Apr 2020 04:27:34: end of X-cor INFO @ Thu, 16 Apr 2020 04:27:34: #2 finished! INFO @ Thu, 16 Apr 2020 04:27:34: #2 predicted fragment length is 194 bps INFO @ Thu, 16 Apr 2020 04:27:34: #2 alternative fragment length(s) may be 194 bps INFO @ Thu, 16 Apr 2020 04:27:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.20_model.r WARNING @ Thu, 16 Apr 2020 04:27:34: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:27:34: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Thu, 16 Apr 2020 04:27:34: #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 04:27:34: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:27:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:27:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448066/SRX6448066.20_summits.bed INFO @ Thu, 16 Apr 2020 04:27:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。