Job ID = 6453883 SRX = SRX1550616 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:52:19 prefetch.2.10.7: 1) Downloading 'SRR3130878'... 2020-06-21T08:52:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:53:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:53:42 prefetch.2.10.7: 'SRR3130878' is valid 2020-06-21T08:53:42 prefetch.2.10.7: 1) 'SRR3130878' was downloaded successfully Read 4000000 spots for SRR3130878/SRR3130878.sra Written 4000000 spots for SRR3130878/SRR3130878.sra 2020-06-21T08:54:05 prefetch.2.10.7: 1) Downloading 'SRR3130879'... 2020-06-21T08:54:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:55:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:55:28 prefetch.2.10.7: 'SRR3130879' is valid 2020-06-21T08:55:28 prefetch.2.10.7: 1) 'SRR3130879' was downloaded successfully Read 4000000 spots for SRR3130879/SRR3130879.sra Written 4000000 spots for SRR3130879/SRR3130879.sra 2020-06-21T08:55:50 prefetch.2.10.7: 1) Downloading 'SRR3130880'... 2020-06-21T08:55:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:44 prefetch.2.10.7: 'SRR3130880' is valid 2020-06-21T08:56:44 prefetch.2.10.7: 1) 'SRR3130880' was downloaded successfully Read 4000000 spots for SRR3130880/SRR3130880.sra Written 4000000 spots for SRR3130880/SRR3130880.sra 2020-06-21T08:57:06 prefetch.2.10.7: 1) Downloading 'SRR3130881'... 2020-06-21T08:57:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:05 prefetch.2.10.7: 'SRR3130881' is valid 2020-06-21T08:58:05 prefetch.2.10.7: 1) 'SRR3130881' was downloaded successfully Read 3695546 spots for SRR3130881/SRR3130881.sra Written 3695546 spots for SRR3130881/SRR3130881.sra 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: 00:03:53 15695546 reads; of these: 15695546 (100.00%) were unpaired; of these: 1365221 (8.70%) aligned 0 times 11407291 (72.68%) aligned exactly 1 time 2923034 (18.62%) aligned >1 times 91.30% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1903228 / 14330325 = 0.1328 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 @ Sun, 21 Jun 2020 18:06:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.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 @ Sun, 21 Jun 2020 18:06:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:16: 1000000 INFO @ Sun, 21 Jun 2020 18:06:23: 2000000 INFO @ Sun, 21 Jun 2020 18:06:30: 3000000 INFO @ Sun, 21 Jun 2020 18:06:36: 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 @ Sun, 21 Jun 2020 18:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.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 @ Sun, 21 Jun 2020 18:06:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:43: 5000000 INFO @ Sun, 21 Jun 2020 18:06:46: 1000000 INFO @ Sun, 21 Jun 2020 18:06:51: 6000000 INFO @ Sun, 21 Jun 2020 18:06:53: 2000000 INFO @ Sun, 21 Jun 2020 18:06:58: 7000000 INFO @ Sun, 21 Jun 2020 18:07:00: 3000000 INFO @ Sun, 21 Jun 2020 18:07:05: 8000000 INFO @ Sun, 21 Jun 2020 18:07:06: 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 @ Sun, 21 Jun 2020 18:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.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 @ Sun, 21 Jun 2020 18:07:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:13: 9000000 INFO @ Sun, 21 Jun 2020 18:07:13: 5000000 INFO @ Sun, 21 Jun 2020 18:07:17: 1000000 INFO @ Sun, 21 Jun 2020 18:07:20: 6000000 INFO @ Sun, 21 Jun 2020 18:07:20: 10000000 INFO @ Sun, 21 Jun 2020 18:07:23: 2000000 INFO @ Sun, 21 Jun 2020 18:07:26: 7000000 INFO @ Sun, 21 Jun 2020 18:07:28: 11000000 INFO @ Sun, 21 Jun 2020 18:07:30: 3000000 INFO @ Sun, 21 Jun 2020 18:07:33: 8000000 INFO @ Sun, 21 Jun 2020 18:07:35: 12000000 INFO @ Sun, 21 Jun 2020 18:07:36: 4000000 INFO @ Sun, 21 Jun 2020 18:07:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:07:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:07:38: #1 total tags in treatment: 12427097 INFO @ Sun, 21 Jun 2020 18:07:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:07:39: #1 tags after filtering in treatment: 12427093 INFO @ Sun, 21 Jun 2020 18:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:39: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:39: 9000000 INFO @ Sun, 21 Jun 2020 18:07:40: #2 number of paired peaks: 357 WARNING @ Sun, 21 Jun 2020 18:07:40: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Sun, 21 Jun 2020 18:07:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:40: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 18:07:40: #2 alternative fragment length(s) may be 4,49,567 bps INFO @ Sun, 21 Jun 2020 18:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.05_model.r WARNING @ Sun, 21 Jun 2020 18:07:40: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:07:40: #2 You may need to consider one of the other alternative d(s): 4,49,567 WARNING @ Sun, 21 Jun 2020 18:07:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:07:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:43: 5000000 INFO @ Sun, 21 Jun 2020 18:07:46: 10000000 INFO @ Sun, 21 Jun 2020 18:07:49: 6000000 INFO @ Sun, 21 Jun 2020 18:07:53: 11000000 INFO @ Sun, 21 Jun 2020 18:07:55: 7000000 INFO @ Sun, 21 Jun 2020 18:07:59: 12000000 INFO @ Sun, 21 Jun 2020 18:08:02: 8000000 INFO @ Sun, 21 Jun 2020 18:08:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:08:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:08:02: #1 total tags in treatment: 12427097 INFO @ Sun, 21 Jun 2020 18:08:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:08:02: #1 tags after filtering in treatment: 12427093 INFO @ Sun, 21 Jun 2020 18:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:03: #2 number of paired peaks: 357 WARNING @ Sun, 21 Jun 2020 18:08:03: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:03: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 18:08:03: #2 alternative fragment length(s) may be 4,49,567 bps INFO @ Sun, 21 Jun 2020 18:08:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.10_model.r WARNING @ Sun, 21 Jun 2020 18:08:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:08:03: #2 You may need to consider one of the other alternative d(s): 4,49,567 WARNING @ Sun, 21 Jun 2020 18:08:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:08:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:08: 9000000 INFO @ Sun, 21 Jun 2020 18:08:13: 10000000 INFO @ Sun, 21 Jun 2020 18:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.05_summits.bed INFO @ Sun, 21 Jun 2020 18:08:15: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (2077 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:08:19: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:25: 12000000 INFO @ Sun, 21 Jun 2020 18:08:28: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:08:28: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:08:28: #1 total tags in treatment: 12427097 INFO @ Sun, 21 Jun 2020 18:08:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:08:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:28: #1 tags after filtering in treatment: 12427093 INFO @ Sun, 21 Jun 2020 18:08:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:29: #2 number of paired peaks: 357 WARNING @ Sun, 21 Jun 2020 18:08:29: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:29: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 18:08:29: #2 alternative fragment length(s) may be 4,49,567 bps INFO @ Sun, 21 Jun 2020 18:08:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.20_model.r WARNING @ Sun, 21 Jun 2020 18:08:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:08:29: #2 You may need to consider one of the other alternative d(s): 4,49,567 WARNING @ Sun, 21 Jun 2020 18:08:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:08:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.10_summits.bed INFO @ Sun, 21 Jun 2020 18:08:40: Done! pass1 - making usageList (410 chroms): 1 millis pass2 - checking and writing primary data (1172 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1550616/SRX1550616.20_summits.bed INFO @ Sun, 21 Jun 2020 18:09:06: Done! pass1 - making usageList (179 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 7 millis CompletedMACS2peakCalling