Job ID = 5721056 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T18:55:14 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 ) 2020-04-15T18:55:14 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 ) 2020-04-15T19:17:51 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 ) spots read : 46,910,508 reads read : 93,821,016 reads written : 93,821,016 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: 00:54:10 46910508 reads; of these: 46910508 (100.00%) were paired; of these: 34007399 (72.49%) aligned concordantly 0 times 9702593 (20.68%) aligned concordantly exactly 1 time 3200516 (6.82%) aligned concordantly >1 times ---- 34007399 pairs aligned concordantly 0 times; of these: 1217465 (3.58%) aligned discordantly 1 time ---- 32789934 pairs aligned 0 times concordantly or discordantly; of these: 65579868 mates make up the pairs; of these: 63883282 (97.41%) aligned 0 times 652809 (1.00%) aligned exactly 1 time 1043777 (1.59%) aligned >1 times 31.91% overall alignment rate Time searching: 00:54:10 Overall time: 00:54:10 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] 11911704 / 14071783 = 0.8465 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 06:33:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.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 06:33:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:33:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:33:19: 1000000 INFO @ Thu, 16 Apr 2020 06:33:26: 2000000 INFO @ Thu, 16 Apr 2020 06:33:33: 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 06:33:40: 4000000 INFO @ Thu, 16 Apr 2020 06:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.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 06:33:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:33:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:33:47: 5000000 INFO @ Thu, 16 Apr 2020 06:33:48: 1000000 INFO @ Thu, 16 Apr 2020 06:33:55: 6000000 INFO @ Thu, 16 Apr 2020 06:33:56: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:33:56: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:33:56: #1 total tags in treatment: 1859218 INFO @ Thu, 16 Apr 2020 06:33:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:33:56: #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 06:33:56: #1 tags after filtering in treatment: 1693160 INFO @ Thu, 16 Apr 2020 06:33:56: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 06:33:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:33:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:33:56: 2000000 INFO @ Thu, 16 Apr 2020 06:33:56: #2 number of paired peaks: 3961 INFO @ Thu, 16 Apr 2020 06:33:56: start model_add_line... INFO @ Thu, 16 Apr 2020 06:33:56: start X-correlation... INFO @ Thu, 16 Apr 2020 06:33:56: end of X-cor INFO @ Thu, 16 Apr 2020 06:33:56: #2 finished! INFO @ Thu, 16 Apr 2020 06:33:56: #2 predicted fragment length is 244 bps INFO @ Thu, 16 Apr 2020 06:33:56: #2 alternative fragment length(s) may be 244 bps INFO @ Thu, 16 Apr 2020 06:33:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.05_model.r WARNING @ Thu, 16 Apr 2020 06:33:56: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:33:56: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Thu, 16 Apr 2020 06:33:56: #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 06:33:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:34:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:34:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.05_summits.bed INFO @ Thu, 16 Apr 2020 06:34:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3598 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:34:03: 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 06:34:10: 4000000 INFO @ Thu, 16 Apr 2020 06:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.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 06:34:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:34:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:34:18: 5000000 INFO @ Thu, 16 Apr 2020 06:34:19: 1000000 INFO @ Thu, 16 Apr 2020 06:34:25: 6000000 INFO @ Thu, 16 Apr 2020 06:34:26: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:34:26: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:34:26: #1 total tags in treatment: 1859218 INFO @ Thu, 16 Apr 2020 06:34:26: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:34:26: #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 06:34:26: #1 tags after filtering in treatment: 1693160 INFO @ Thu, 16 Apr 2020 06:34:26: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 06:34:26: #1 finished! INFO @ Thu, 16 Apr 2020 06:34:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:34:26: 2000000 INFO @ Thu, 16 Apr 2020 06:34:26: #2 number of paired peaks: 3961 INFO @ Thu, 16 Apr 2020 06:34:26: start model_add_line... INFO @ Thu, 16 Apr 2020 06:34:26: start X-correlation... INFO @ Thu, 16 Apr 2020 06:34:26: end of X-cor INFO @ Thu, 16 Apr 2020 06:34:26: #2 finished! INFO @ Thu, 16 Apr 2020 06:34:26: #2 predicted fragment length is 244 bps INFO @ Thu, 16 Apr 2020 06:34:26: #2 alternative fragment length(s) may be 244 bps INFO @ Thu, 16 Apr 2020 06:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.10_model.r WARNING @ Thu, 16 Apr 2020 06:34:26: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:34:26: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Thu, 16 Apr 2020 06:34:26: #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 06:34:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:34:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:34:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:34:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:34:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:34:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.10_summits.bed INFO @ Thu, 16 Apr 2020 06:34:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2417 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:34:34: 3000000 INFO @ Thu, 16 Apr 2020 06:34:41: 4000000 INFO @ Thu, 16 Apr 2020 06:34:48: 5000000 INFO @ Thu, 16 Apr 2020 06:34:55: 6000000 INFO @ Thu, 16 Apr 2020 06:34:56: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 06:34:56: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 06:34:56: #1 total tags in treatment: 1859218 INFO @ Thu, 16 Apr 2020 06:34:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:34:56: #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 06:34:56: #1 tags after filtering in treatment: 1693160 INFO @ Thu, 16 Apr 2020 06:34:56: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 16 Apr 2020 06:34:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:34:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:34:56: #2 number of paired peaks: 3961 INFO @ Thu, 16 Apr 2020 06:34:56: start model_add_line... INFO @ Thu, 16 Apr 2020 06:34:56: start X-correlation... INFO @ Thu, 16 Apr 2020 06:34:56: end of X-cor INFO @ Thu, 16 Apr 2020 06:34:56: #2 finished! INFO @ Thu, 16 Apr 2020 06:34:56: #2 predicted fragment length is 244 bps INFO @ Thu, 16 Apr 2020 06:34:56: #2 alternative fragment length(s) may be 244 bps INFO @ Thu, 16 Apr 2020 06:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.20_model.r WARNING @ Thu, 16 Apr 2020 06:34:56: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:34:56: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Thu, 16 Apr 2020 06:34:56: #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 06:34:56: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:35:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:35:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:35:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:35:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386787/SRX6386787.20_summits.bed INFO @ Thu, 16 Apr 2020 06:35:03: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (1242 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。