Job ID = 5720930 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T18:17:47 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 ) 2020-04-15T19:02:37 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 ) 2020-04-15T19:03:45 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 ) 2020-04-15T19:05:39 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 ) 2020-04-15T19:10:35 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 : 35,000,323 reads read : 70,000,646 reads written : 70,000,646 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: 01:13:30 35000323 reads; of these: 35000323 (100.00%) were paired; of these: 14667097 (41.91%) aligned concordantly 0 times 15591543 (44.55%) aligned concordantly exactly 1 time 4741683 (13.55%) aligned concordantly >1 times ---- 14667097 pairs aligned concordantly 0 times; of these: 1083606 (7.39%) aligned discordantly 1 time ---- 13583491 pairs aligned 0 times concordantly or discordantly; of these: 27166982 mates make up the pairs; of these: 25681721 (94.53%) aligned 0 times 628824 (2.31%) aligned exactly 1 time 856437 (3.15%) aligned >1 times 63.31% overall alignment rate Time searching: 01:13:30 Overall time: 01:13:30 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 36 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] 17653748 / 21342652 = 0.8272 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 05:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.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 05:57:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:57:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:57:36: 1000000 INFO @ Thu, 16 Apr 2020 05:57:45: 2000000 INFO @ Thu, 16 Apr 2020 05:57:54: 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 05:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.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 05:57:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:57:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:03: 4000000 INFO @ Thu, 16 Apr 2020 05:58:05: 1000000 INFO @ Thu, 16 Apr 2020 05:58:12: 5000000 INFO @ Thu, 16 Apr 2020 05:58:15: 2000000 INFO @ Thu, 16 Apr 2020 05:58:22: 6000000 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 05:58:25: 3000000 INFO @ Thu, 16 Apr 2020 05:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.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 05:58:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:58:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:58:31: 7000000 INFO @ Thu, 16 Apr 2020 05:58:35: 1000000 INFO @ Thu, 16 Apr 2020 05:58:35: 4000000 INFO @ Thu, 16 Apr 2020 05:58:41: 8000000 INFO @ Thu, 16 Apr 2020 05:58:43: 2000000 INFO @ Thu, 16 Apr 2020 05:58:45: 5000000 INFO @ Thu, 16 Apr 2020 05:58:50: 9000000 INFO @ Thu, 16 Apr 2020 05:58:50: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 05:58:50: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 05:58:50: #1 total tags in treatment: 3295718 INFO @ Thu, 16 Apr 2020 05:58:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:58:50: #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 05:58:50: #1 tags after filtering in treatment: 3105735 INFO @ Thu, 16 Apr 2020 05:58:50: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:58:50: #1 finished! INFO @ Thu, 16 Apr 2020 05:58:50: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:58:51: #2 number of paired peaks: 3616 INFO @ Thu, 16 Apr 2020 05:58:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:58:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:58:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:58:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:58:51: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 05:58:51: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 05:58:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.05_model.r WARNING @ Thu, 16 Apr 2020 05:58:51: #2 Since the d (245) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:58:51: #2 You may need to consider one of the other alternative d(s): 245 WARNING @ Thu, 16 Apr 2020 05:58:51: #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 05:58:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:58:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:58:52: 3000000 INFO @ Thu, 16 Apr 2020 05:58:55: 6000000 INFO @ Thu, 16 Apr 2020 05:58:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:00: 4000000 INFO @ Thu, 16 Apr 2020 05:59:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.05_summits.bed INFO @ Thu, 16 Apr 2020 05:59:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5445 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:59:04: 7000000 INFO @ Thu, 16 Apr 2020 05:59:08: 5000000 INFO @ Thu, 16 Apr 2020 05:59:14: 8000000 INFO @ Thu, 16 Apr 2020 05:59:16: 6000000 INFO @ Thu, 16 Apr 2020 05:59:23: 9000000 INFO @ Thu, 16 Apr 2020 05:59:24: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 05:59:24: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 05:59:24: #1 total tags in treatment: 3295718 INFO @ Thu, 16 Apr 2020 05:59:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:24: #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 05:59:24: #1 tags after filtering in treatment: 3105735 INFO @ Thu, 16 Apr 2020 05:59:24: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:59:24: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:24: 7000000 INFO @ Thu, 16 Apr 2020 05:59:24: #2 number of paired peaks: 3616 INFO @ Thu, 16 Apr 2020 05:59:24: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:24: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:24: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:24: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:24: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 05:59:24: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 05:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.10_model.r WARNING @ Thu, 16 Apr 2020 05:59:24: #2 Since the d (245) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:59:24: #2 You may need to consider one of the other alternative d(s): 245 WARNING @ Thu, 16 Apr 2020 05:59:24: #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 05:59:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:31: 8000000 INFO @ Thu, 16 Apr 2020 05:59:32: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.10_summits.bed INFO @ Thu, 16 Apr 2020 05:59:36: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (3092 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:59:39: 9000000 INFO @ Thu, 16 Apr 2020 05:59:39: #1 tag size is determined as 151 bps INFO @ Thu, 16 Apr 2020 05:59:39: #1 tag size = 151 INFO @ Thu, 16 Apr 2020 05:59:39: #1 total tags in treatment: 3295718 INFO @ Thu, 16 Apr 2020 05:59:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:59:39: #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 05:59:39: #1 tags after filtering in treatment: 3105735 INFO @ Thu, 16 Apr 2020 05:59:39: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 05:59:39: #1 finished! INFO @ Thu, 16 Apr 2020 05:59:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:59:39: #2 number of paired peaks: 3616 INFO @ Thu, 16 Apr 2020 05:59:39: start model_add_line... INFO @ Thu, 16 Apr 2020 05:59:39: start X-correlation... INFO @ Thu, 16 Apr 2020 05:59:40: end of X-cor INFO @ Thu, 16 Apr 2020 05:59:40: #2 finished! INFO @ Thu, 16 Apr 2020 05:59:40: #2 predicted fragment length is 245 bps INFO @ Thu, 16 Apr 2020 05:59:40: #2 alternative fragment length(s) may be 245 bps INFO @ Thu, 16 Apr 2020 05:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.20_model.r WARNING @ Thu, 16 Apr 2020 05:59:40: #2 Since the d (245) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:59:40: #2 You may need to consider one of the other alternative d(s): 245 WARNING @ Thu, 16 Apr 2020 05:59:40: #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 05:59:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:59:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6386731/SRX6386731.20_summits.bed INFO @ Thu, 16 Apr 2020 05:59:51: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1268 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。