Job ID = 5720786 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:25:55 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 ) 2020-04-15T16:25:55 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 ) 2020-04-15T16:25:55 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 ) 2020-04-15T16:25:55 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 ) 2020-04-15T16:25:55 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 : 6,310,604 reads read : 12,621,208 reads written : 12,621,208 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: 00:18:29 6310604 reads; of these: 6310604 (100.00%) were paired; of these: 1123482 (17.80%) aligned concordantly 0 times 3787197 (60.01%) aligned concordantly exactly 1 time 1399925 (22.18%) aligned concordantly >1 times ---- 1123482 pairs aligned concordantly 0 times; of these: 350932 (31.24%) aligned discordantly 1 time ---- 772550 pairs aligned 0 times concordantly or discordantly; of these: 1545100 mates make up the pairs; of these: 744572 (48.19%) aligned 0 times 403441 (26.11%) aligned exactly 1 time 397087 (25.70%) aligned >1 times 94.10% overall alignment rate Time searching: 00:18:29 Overall time: 00:18:29 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] 914405 / 5338574 = 0.1713 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 01:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.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 01:55:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:55:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:55:26: 1000000 INFO @ Thu, 16 Apr 2020 01:55:33: 2000000 INFO @ Thu, 16 Apr 2020 01:55:39: 3000000 INFO @ Thu, 16 Apr 2020 01:55:46: 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 01:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.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 01:55:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:55:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:55:53: 5000000 INFO @ Thu, 16 Apr 2020 01:55:56: 1000000 INFO @ Thu, 16 Apr 2020 01:56:00: 6000000 INFO @ Thu, 16 Apr 2020 01:56:02: 2000000 INFO @ Thu, 16 Apr 2020 01:56:07: 7000000 INFO @ Thu, 16 Apr 2020 01:56:08: 3000000 INFO @ Thu, 16 Apr 2020 01:56:14: 8000000 INFO @ Thu, 16 Apr 2020 01:56:14: 4000000 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 01:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.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 01:56:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:56:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:56:20: 5000000 INFO @ Thu, 16 Apr 2020 01:56:21: 9000000 INFO @ Thu, 16 Apr 2020 01:56:26: 1000000 INFO @ Thu, 16 Apr 2020 01:56:26: 6000000 INFO @ Thu, 16 Apr 2020 01:56:28: 10000000 INFO @ Thu, 16 Apr 2020 01:56:28: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 01:56:28: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 01:56:28: #1 total tags in treatment: 4298822 INFO @ Thu, 16 Apr 2020 01:56:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:56:28: #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 01:56:28: #1 tags after filtering in treatment: 4153748 INFO @ Thu, 16 Apr 2020 01:56:28: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 01:56:28: #1 finished! INFO @ Thu, 16 Apr 2020 01:56:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:56:29: #2 number of paired peaks: 308 WARNING @ Thu, 16 Apr 2020 01:56:29: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Thu, 16 Apr 2020 01:56:29: start model_add_line... INFO @ Thu, 16 Apr 2020 01:56:29: start X-correlation... INFO @ Thu, 16 Apr 2020 01:56:29: end of X-cor INFO @ Thu, 16 Apr 2020 01:56:29: #2 finished! INFO @ Thu, 16 Apr 2020 01:56:29: #2 predicted fragment length is 159 bps INFO @ Thu, 16 Apr 2020 01:56:29: #2 alternative fragment length(s) may be 159 bps INFO @ Thu, 16 Apr 2020 01:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.05_model.r WARNING @ Thu, 16 Apr 2020 01:56:29: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:56:29: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Thu, 16 Apr 2020 01:56:29: #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 01:56:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:56:32: 2000000 INFO @ Thu, 16 Apr 2020 01:56:32: 7000000 INFO @ Thu, 16 Apr 2020 01:56:38: 3000000 INFO @ Thu, 16 Apr 2020 01:56:38: 8000000 INFO @ Thu, 16 Apr 2020 01:56:38: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:56:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:56:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:56:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.05_summits.bed INFO @ Thu, 16 Apr 2020 01:56:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1482 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:56:44: 9000000 INFO @ Thu, 16 Apr 2020 01:56:44: 4000000 INFO @ Thu, 16 Apr 2020 01:56:50: 10000000 INFO @ Thu, 16 Apr 2020 01:56:50: 5000000 INFO @ Thu, 16 Apr 2020 01:56:50: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 01:56:50: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 01:56:50: #1 total tags in treatment: 4298822 INFO @ Thu, 16 Apr 2020 01:56:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:56:50: #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 01:56:50: #1 tags after filtering in treatment: 4153748 INFO @ Thu, 16 Apr 2020 01:56:50: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 01:56:50: #1 finished! INFO @ Thu, 16 Apr 2020 01:56:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:56:51: #2 number of paired peaks: 308 WARNING @ Thu, 16 Apr 2020 01:56:51: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Thu, 16 Apr 2020 01:56:51: start model_add_line... INFO @ Thu, 16 Apr 2020 01:56:51: start X-correlation... INFO @ Thu, 16 Apr 2020 01:56:51: end of X-cor INFO @ Thu, 16 Apr 2020 01:56:51: #2 finished! INFO @ Thu, 16 Apr 2020 01:56:51: #2 predicted fragment length is 159 bps INFO @ Thu, 16 Apr 2020 01:56:51: #2 alternative fragment length(s) may be 159 bps INFO @ Thu, 16 Apr 2020 01:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.10_model.r WARNING @ Thu, 16 Apr 2020 01:56:51: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:56:51: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Thu, 16 Apr 2020 01:56:51: #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 01:56:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:56:56: 6000000 INFO @ Thu, 16 Apr 2020 01:56:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:57:02: 7000000 INFO @ Thu, 16 Apr 2020 01:57:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:57:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:57:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.10_summits.bed INFO @ Thu, 16 Apr 2020 01:57:04: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:57:08: 8000000 INFO @ Thu, 16 Apr 2020 01:57:14: 9000000 INFO @ Thu, 16 Apr 2020 01:57:19: 10000000 INFO @ Thu, 16 Apr 2020 01:57:20: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 01:57:20: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 01:57:20: #1 total tags in treatment: 4298822 INFO @ Thu, 16 Apr 2020 01:57:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:57:20: #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 01:57:20: #1 tags after filtering in treatment: 4153748 INFO @ Thu, 16 Apr 2020 01:57:20: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 01:57:20: #1 finished! INFO @ Thu, 16 Apr 2020 01:57:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:57:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:57:20: #2 number of paired peaks: 308 WARNING @ Thu, 16 Apr 2020 01:57:20: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Thu, 16 Apr 2020 01:57:20: start model_add_line... INFO @ Thu, 16 Apr 2020 01:57:20: start X-correlation... INFO @ Thu, 16 Apr 2020 01:57:20: end of X-cor INFO @ Thu, 16 Apr 2020 01:57:20: #2 finished! INFO @ Thu, 16 Apr 2020 01:57:20: #2 predicted fragment length is 159 bps INFO @ Thu, 16 Apr 2020 01:57:20: #2 alternative fragment length(s) may be 159 bps INFO @ Thu, 16 Apr 2020 01:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.20_model.r WARNING @ Thu, 16 Apr 2020 01:57:20: #2 Since the d (159) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:57:20: #2 You may need to consider one of the other alternative d(s): 159 WARNING @ Thu, 16 Apr 2020 01:57:20: #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 01:57:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:57:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:57:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:57:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:57:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:57:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246879/SRX5246879.20_summits.bed INFO @ Thu, 16 Apr 2020 01:57:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (419 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。