Job ID = 5720779 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T16:29:59 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 ) 2020-04-15T16:29:59 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 : 17,705,088 reads read : 35,410,176 reads written : 35,410,176 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: 00:51:48 17705088 reads; of these: 17705088 (100.00%) were paired; of these: 3445345 (19.46%) aligned concordantly 0 times 10385991 (58.66%) aligned concordantly exactly 1 time 3873752 (21.88%) aligned concordantly >1 times ---- 3445345 pairs aligned concordantly 0 times; of these: 1149347 (33.36%) aligned discordantly 1 time ---- 2295998 pairs aligned 0 times concordantly or discordantly; of these: 4591996 mates make up the pairs; of these: 2226366 (48.48%) aligned 0 times 1136780 (24.76%) aligned exactly 1 time 1228850 (26.76%) aligned >1 times 93.71% overall alignment rate Time searching: 00:51:48 Overall time: 00:51:48 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] 4142499 / 14744096 = 0.2810 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 02:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.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 02:40:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:40:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:40:58: 1000000 INFO @ Thu, 16 Apr 2020 02:41:04: 2000000 INFO @ Thu, 16 Apr 2020 02:41:09: 3000000 INFO @ Thu, 16 Apr 2020 02:41:15: 4000000 INFO @ Thu, 16 Apr 2020 02:41:21: 5000000 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 02:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.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 02:41:23: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:41:23: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:41:26: 6000000 INFO @ Thu, 16 Apr 2020 02:41:29: 1000000 INFO @ Thu, 16 Apr 2020 02:41:33: 7000000 INFO @ Thu, 16 Apr 2020 02:41:35: 2000000 INFO @ Thu, 16 Apr 2020 02:41:39: 8000000 INFO @ Thu, 16 Apr 2020 02:41:42: 3000000 INFO @ Thu, 16 Apr 2020 02:41:45: 9000000 INFO @ Thu, 16 Apr 2020 02:41:48: 4000000 BedGraph に変換中... INFO @ Thu, 16 Apr 2020 02:41:51: 10000000 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 02:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.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 02:41:53: #1 read tag files... INFO @ Thu, 16 Apr 2020 02:41:53: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 02:41:54: 5000000 INFO @ Thu, 16 Apr 2020 02:41:57: 11000000 INFO @ Thu, 16 Apr 2020 02:42:00: 1000000 INFO @ Thu, 16 Apr 2020 02:42:00: 6000000 INFO @ Thu, 16 Apr 2020 02:42:03: 12000000 INFO @ Thu, 16 Apr 2020 02:42:06: 7000000 INFO @ Thu, 16 Apr 2020 02:42:08: 2000000 INFO @ Thu, 16 Apr 2020 02:42:10: 13000000 INFO @ Thu, 16 Apr 2020 02:42:13: 8000000 INFO @ Thu, 16 Apr 2020 02:42:15: 3000000 INFO @ Thu, 16 Apr 2020 02:42:16: 14000000 INFO @ Thu, 16 Apr 2020 02:42:19: 9000000 INFO @ Thu, 16 Apr 2020 02:42:22: 15000000 INFO @ Thu, 16 Apr 2020 02:42:23: 4000000 INFO @ Thu, 16 Apr 2020 02:42:25: 10000000 INFO @ Thu, 16 Apr 2020 02:42:28: 16000000 INFO @ Thu, 16 Apr 2020 02:42:30: 5000000 INFO @ Thu, 16 Apr 2020 02:42:31: 11000000 INFO @ Thu, 16 Apr 2020 02:42:34: 17000000 INFO @ Thu, 16 Apr 2020 02:42:37: 12000000 INFO @ Thu, 16 Apr 2020 02:42:38: 6000000 INFO @ Thu, 16 Apr 2020 02:42:41: 18000000 INFO @ Thu, 16 Apr 2020 02:42:44: 13000000 INFO @ Thu, 16 Apr 2020 02:42:45: 7000000 INFO @ Thu, 16 Apr 2020 02:42:47: 19000000 INFO @ Thu, 16 Apr 2020 02:42:50: 14000000 INFO @ Thu, 16 Apr 2020 02:42:53: 8000000 INFO @ Thu, 16 Apr 2020 02:42:53: 20000000 INFO @ Thu, 16 Apr 2020 02:42:56: 15000000 INFO @ Thu, 16 Apr 2020 02:43:00: 21000000 INFO @ Thu, 16 Apr 2020 02:43:00: 9000000 INFO @ Thu, 16 Apr 2020 02:43:02: 16000000 INFO @ Thu, 16 Apr 2020 02:43:07: 22000000 INFO @ Thu, 16 Apr 2020 02:43:08: 10000000 INFO @ Thu, 16 Apr 2020 02:43:08: 17000000 INFO @ Thu, 16 Apr 2020 02:43:13: 23000000 INFO @ Thu, 16 Apr 2020 02:43:14: 18000000 INFO @ Thu, 16 Apr 2020 02:43:15: 11000000 INFO @ Thu, 16 Apr 2020 02:43:19: 24000000 INFO @ Thu, 16 Apr 2020 02:43:21: 19000000 INFO @ Thu, 16 Apr 2020 02:43:22: 12000000 INFO @ Thu, 16 Apr 2020 02:43:25: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:43:25: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:43:25: #1 total tags in treatment: 10251970 INFO @ Thu, 16 Apr 2020 02:43:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:43:25: #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 02:43:25: #1 tags after filtering in treatment: 9656769 INFO @ Thu, 16 Apr 2020 02:43:25: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 02:43:25: #1 finished! INFO @ Thu, 16 Apr 2020 02:43:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:43:26: #2 number of paired peaks: 259 WARNING @ Thu, 16 Apr 2020 02:43:26: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Thu, 16 Apr 2020 02:43:26: start model_add_line... INFO @ Thu, 16 Apr 2020 02:43:26: start X-correlation... INFO @ Thu, 16 Apr 2020 02:43:26: end of X-cor INFO @ Thu, 16 Apr 2020 02:43:26: #2 finished! INFO @ Thu, 16 Apr 2020 02:43:26: #2 predicted fragment length is 144 bps INFO @ Thu, 16 Apr 2020 02:43:26: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 16 Apr 2020 02:43:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.05_model.r WARNING @ Thu, 16 Apr 2020 02:43:26: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:43:26: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Thu, 16 Apr 2020 02:43:26: #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 02:43:26: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:43:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:43:27: 20000000 INFO @ Thu, 16 Apr 2020 02:43:30: 13000000 INFO @ Thu, 16 Apr 2020 02:43:33: 21000000 INFO @ Thu, 16 Apr 2020 02:43:37: 14000000 INFO @ Thu, 16 Apr 2020 02:43:40: 22000000 INFO @ Thu, 16 Apr 2020 02:43:44: 15000000 INFO @ Thu, 16 Apr 2020 02:43:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:43:46: 23000000 INFO @ Thu, 16 Apr 2020 02:43:51: 16000000 INFO @ Thu, 16 Apr 2020 02:43:52: 24000000 INFO @ Thu, 16 Apr 2020 02:43:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.05_peaks.xls INFO @ Thu, 16 Apr 2020 02:43:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:43:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.05_summits.bed INFO @ Thu, 16 Apr 2020 02:43:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2331 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:43:58: 17000000 INFO @ Thu, 16 Apr 2020 02:43:58: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:43:58: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:43:58: #1 total tags in treatment: 10251970 INFO @ Thu, 16 Apr 2020 02:43:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:43:58: #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 02:43:58: #1 tags after filtering in treatment: 9656769 INFO @ Thu, 16 Apr 2020 02:43:58: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 02:43:58: #1 finished! INFO @ Thu, 16 Apr 2020 02:43:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:43:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:43:59: #2 number of paired peaks: 259 WARNING @ Thu, 16 Apr 2020 02:43:59: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Thu, 16 Apr 2020 02:43:59: start model_add_line... INFO @ Thu, 16 Apr 2020 02:43:59: start X-correlation... INFO @ Thu, 16 Apr 2020 02:43:59: end of X-cor INFO @ Thu, 16 Apr 2020 02:43:59: #2 finished! INFO @ Thu, 16 Apr 2020 02:43:59: #2 predicted fragment length is 144 bps INFO @ Thu, 16 Apr 2020 02:43:59: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 16 Apr 2020 02:43:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.10_model.r WARNING @ Thu, 16 Apr 2020 02:43:59: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:43:59: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Thu, 16 Apr 2020 02:43:59: #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 02:43:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:43:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:44:05: 18000000 INFO @ Thu, 16 Apr 2020 02:44:12: 19000000 INFO @ Thu, 16 Apr 2020 02:44:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:44:19: 20000000 INFO @ Thu, 16 Apr 2020 02:44:26: 21000000 INFO @ Thu, 16 Apr 2020 02:44:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.10_peaks.xls INFO @ Thu, 16 Apr 2020 02:44:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:44:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.10_summits.bed INFO @ Thu, 16 Apr 2020 02:44:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1412 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 02:44:34: 22000000 INFO @ Thu, 16 Apr 2020 02:44:41: 23000000 INFO @ Thu, 16 Apr 2020 02:44:48: 24000000 INFO @ Thu, 16 Apr 2020 02:44:54: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 02:44:54: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 02:44:54: #1 total tags in treatment: 10251970 INFO @ Thu, 16 Apr 2020 02:44:54: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 02:44:54: #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 02:44:54: #1 tags after filtering in treatment: 9656769 INFO @ Thu, 16 Apr 2020 02:44:54: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 16 Apr 2020 02:44:54: #1 finished! INFO @ Thu, 16 Apr 2020 02:44:54: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 02:44:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 02:44:55: #2 number of paired peaks: 259 WARNING @ Thu, 16 Apr 2020 02:44:55: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Thu, 16 Apr 2020 02:44:55: start model_add_line... INFO @ Thu, 16 Apr 2020 02:44:55: start X-correlation... INFO @ Thu, 16 Apr 2020 02:44:55: end of X-cor INFO @ Thu, 16 Apr 2020 02:44:55: #2 finished! INFO @ Thu, 16 Apr 2020 02:44:55: #2 predicted fragment length is 144 bps INFO @ Thu, 16 Apr 2020 02:44:55: #2 alternative fragment length(s) may be 144 bps INFO @ Thu, 16 Apr 2020 02:44:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.20_model.r WARNING @ Thu, 16 Apr 2020 02:44:55: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 02:44:55: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Thu, 16 Apr 2020 02:44:55: #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 02:44:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 02:44:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 02:45:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 02:45:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.20_peaks.xls INFO @ Thu, 16 Apr 2020 02:45:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 02:45:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246872/SRX5246872.20_summits.bed INFO @ Thu, 16 Apr 2020 02:45:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (805 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。