Job ID = 5720891 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T17:55:50 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 ) 2020-04-15T17:59:20 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 : 17,383,638 reads read : 17,383,638 reads written : 17,383,638 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: 00:07:15 17383638 reads; of these: 17383638 (100.00%) were unpaired; of these: 1226894 (7.06%) aligned 0 times 10995241 (63.25%) aligned exactly 1 time 5161503 (29.69%) aligned >1 times 92.94% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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_rmdupse_core] 9186002 / 16156744 = 0.5686 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 03:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.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 03:11:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:11:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:11:56: 1000000 INFO @ Thu, 16 Apr 2020 03:12:02: 2000000 INFO @ Thu, 16 Apr 2020 03:12:09: 3000000 INFO @ Thu, 16 Apr 2020 03:12:15: 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 03:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.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 03:12:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:12:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:12:22: 5000000 INFO @ Thu, 16 Apr 2020 03:12:29: 1000000 INFO @ Thu, 16 Apr 2020 03:12:30: 6000000 INFO @ Thu, 16 Apr 2020 03:12:37: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:12:37: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:12:37: #1 total tags in treatment: 6970742 INFO @ Thu, 16 Apr 2020 03:12:37: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:12:37: #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 03:12:38: #1 tags after filtering in treatment: 6970742 INFO @ Thu, 16 Apr 2020 03:12:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:12:38: #1 finished! INFO @ Thu, 16 Apr 2020 03:12:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:12:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:12:38: 2000000 INFO @ Thu, 16 Apr 2020 03:12:38: #2 number of paired peaks: 394 WARNING @ Thu, 16 Apr 2020 03:12:38: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Thu, 16 Apr 2020 03:12:38: start model_add_line... INFO @ Thu, 16 Apr 2020 03:12:38: start X-correlation... INFO @ Thu, 16 Apr 2020 03:12:38: end of X-cor INFO @ Thu, 16 Apr 2020 03:12:38: #2 finished! INFO @ Thu, 16 Apr 2020 03:12:38: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:12:38: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.05_model.r WARNING @ Thu, 16 Apr 2020 03:12:38: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:12:38: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:12:38: #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 03:12:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:12:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:12:45: 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 03:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.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 03:12:50: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:12:50: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 03:12:52: 4000000 INFO @ Thu, 16 Apr 2020 03:12:52: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:12:57: 1000000 INFO @ Thu, 16 Apr 2020 03:12:59: 5000000 INFO @ Thu, 16 Apr 2020 03:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.05_peaks.xls INFO @ Thu, 16 Apr 2020 03:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.05_summits.bed INFO @ Thu, 16 Apr 2020 03:12:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3492 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:13:04: 2000000 INFO @ Thu, 16 Apr 2020 03:13:06: 6000000 INFO @ Thu, 16 Apr 2020 03:13:12: 3000000 INFO @ Thu, 16 Apr 2020 03:13:13: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:13:13: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:13:13: #1 total tags in treatment: 6970742 INFO @ Thu, 16 Apr 2020 03:13:13: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:13:13: #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 03:13:14: #1 tags after filtering in treatment: 6970742 INFO @ Thu, 16 Apr 2020 03:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:13:14: #1 finished! INFO @ Thu, 16 Apr 2020 03:13:14: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:13:14: #2 number of paired peaks: 394 WARNING @ Thu, 16 Apr 2020 03:13:14: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Thu, 16 Apr 2020 03:13:14: start model_add_line... INFO @ Thu, 16 Apr 2020 03:13:14: start X-correlation... INFO @ Thu, 16 Apr 2020 03:13:14: end of X-cor INFO @ Thu, 16 Apr 2020 03:13:14: #2 finished! INFO @ Thu, 16 Apr 2020 03:13:14: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:13:14: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:13:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.10_model.r WARNING @ Thu, 16 Apr 2020 03:13:14: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:13:14: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:13:14: #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 03:13:14: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:13:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:13:19: 4000000 INFO @ Thu, 16 Apr 2020 03:13:25: 5000000 INFO @ Thu, 16 Apr 2020 03:13:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:13:32: 6000000 INFO @ Thu, 16 Apr 2020 03:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.10_peaks.xls INFO @ Thu, 16 Apr 2020 03:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.10_summits.bed INFO @ Thu, 16 Apr 2020 03:13:37: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1316 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 03:13:38: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 03:13:38: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 03:13:38: #1 total tags in treatment: 6970742 INFO @ Thu, 16 Apr 2020 03:13:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 03:13:38: #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 03:13:38: #1 tags after filtering in treatment: 6970742 INFO @ Thu, 16 Apr 2020 03:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 03:13:38: #1 finished! INFO @ Thu, 16 Apr 2020 03:13:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 03:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 03:13:39: #2 number of paired peaks: 394 WARNING @ Thu, 16 Apr 2020 03:13:39: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Thu, 16 Apr 2020 03:13:39: start model_add_line... INFO @ Thu, 16 Apr 2020 03:13:39: start X-correlation... INFO @ Thu, 16 Apr 2020 03:13:39: end of X-cor INFO @ Thu, 16 Apr 2020 03:13:39: #2 finished! INFO @ Thu, 16 Apr 2020 03:13:39: #2 predicted fragment length is 73 bps INFO @ Thu, 16 Apr 2020 03:13:39: #2 alternative fragment length(s) may be 73 bps INFO @ Thu, 16 Apr 2020 03:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.20_model.r WARNING @ Thu, 16 Apr 2020 03:13:39: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 03:13:39: #2 You may need to consider one of the other alternative d(s): 73 WARNING @ Thu, 16 Apr 2020 03:13:39: #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 03:13:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 03:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 03:13:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 03:14:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.20_peaks.xls INFO @ Thu, 16 Apr 2020 03:14:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 03:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5775919/SRX5775919.20_summits.bed INFO @ Thu, 16 Apr 2020 03:14:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (487 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。