Job ID = 6456814 SRX = SRX3981705 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:13:24 prefetch.2.10.7: 1) Downloading 'SRR7050515'... 2020-06-21T11:13:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:15:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:15:13 prefetch.2.10.7: 'SRR7050515' is valid 2020-06-21T11:15:13 prefetch.2.10.7: 1) 'SRR7050515' was downloaded successfully 2020-06-21T11:15:13 prefetch.2.10.7: 'SRR7050515' has 0 unresolved dependencies Read 6954252 spots for SRR7050515/SRR7050515.sra Written 6954252 spots for SRR7050515/SRR7050515.sra 2020-06-21T11:15:45 prefetch.2.10.7: 1) Downloading 'SRR7050516'... 2020-06-21T11:15:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:16:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:16:42 prefetch.2.10.7: 'SRR7050516' is valid 2020-06-21T11:16:42 prefetch.2.10.7: 1) 'SRR7050516' was downloaded successfully 2020-06-21T11:16:42 prefetch.2.10.7: 'SRR7050516' has 0 unresolved dependencies Read 6944475 spots for SRR7050516/SRR7050516.sra Written 6944475 spots for SRR7050516/SRR7050516.sra 2020-06-21T11:17:18 prefetch.2.10.7: 1) Downloading 'SRR7050517'... 2020-06-21T11:17:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:17:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:17:52 prefetch.2.10.7: 'SRR7050517' is valid 2020-06-21T11:17:52 prefetch.2.10.7: 1) 'SRR7050517' was downloaded successfully 2020-06-21T11:17:52 prefetch.2.10.7: 'SRR7050517' has 0 unresolved dependencies Read 6977943 spots for SRR7050517/SRR7050517.sra Written 6977943 spots for SRR7050517/SRR7050517.sra 2020-06-21T11:18:25 prefetch.2.10.7: 1) Downloading 'SRR7050518'... 2020-06-21T11:18:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:19:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:19:43 prefetch.2.10.7: 'SRR7050518' is valid 2020-06-21T11:19:43 prefetch.2.10.7: 1) 'SRR7050518' was downloaded successfully 2020-06-21T11:19:43 prefetch.2.10.7: 'SRR7050518' has 0 unresolved dependencies Read 7005644 spots for SRR7050518/SRR7050518.sra Written 7005644 spots for SRR7050518/SRR7050518.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: 00:07:25 27882314 reads; of these: 27882314 (100.00%) were unpaired; of these: 1227215 (4.40%) aligned 0 times 19559285 (70.15%) aligned exactly 1 time 7095814 (25.45%) aligned >1 times 95.60% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 12 files... [bam_rmdupse_core] 3751207 / 26655099 = 0.1407 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 20:33:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.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 20:33:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:39: 1000000 INFO @ Sun, 21 Jun 2020 20:33:45: 2000000 INFO @ Sun, 21 Jun 2020 20:33:52: 3000000 INFO @ Sun, 21 Jun 2020 20:33:58: 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 20:34:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.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 20:34:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:04: 5000000 INFO @ Sun, 21 Jun 2020 20:34:09: 1000000 INFO @ Sun, 21 Jun 2020 20:34:10: 6000000 INFO @ Sun, 21 Jun 2020 20:34:15: 2000000 INFO @ Sun, 21 Jun 2020 20:34:17: 7000000 INFO @ Sun, 21 Jun 2020 20:34:21: 3000000 INFO @ Sun, 21 Jun 2020 20:34:23: 8000000 INFO @ Sun, 21 Jun 2020 20:34:26: 4000000 INFO @ Sun, 21 Jun 2020 20:34:30: 9000000 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 20:34:32: 5000000 INFO @ Sun, 21 Jun 2020 20:34:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.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 20:34:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:34:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:34:36: 10000000 INFO @ Sun, 21 Jun 2020 20:34:37: 6000000 INFO @ Sun, 21 Jun 2020 20:34:39: 1000000 INFO @ Sun, 21 Jun 2020 20:34:43: 11000000 INFO @ Sun, 21 Jun 2020 20:34:43: 7000000 INFO @ Sun, 21 Jun 2020 20:34:44: 2000000 INFO @ Sun, 21 Jun 2020 20:34:49: 12000000 INFO @ Sun, 21 Jun 2020 20:34:49: 8000000 INFO @ Sun, 21 Jun 2020 20:34:50: 3000000 INFO @ Sun, 21 Jun 2020 20:34:55: 9000000 INFO @ Sun, 21 Jun 2020 20:34:55: 13000000 INFO @ Sun, 21 Jun 2020 20:34:56: 4000000 INFO @ Sun, 21 Jun 2020 20:35:00: 10000000 INFO @ Sun, 21 Jun 2020 20:35:01: 5000000 INFO @ Sun, 21 Jun 2020 20:35:02: 14000000 INFO @ Sun, 21 Jun 2020 20:35:06: 11000000 INFO @ Sun, 21 Jun 2020 20:35:07: 6000000 INFO @ Sun, 21 Jun 2020 20:35:08: 15000000 INFO @ Sun, 21 Jun 2020 20:35:12: 12000000 INFO @ Sun, 21 Jun 2020 20:35:13: 7000000 INFO @ Sun, 21 Jun 2020 20:35:15: 16000000 INFO @ Sun, 21 Jun 2020 20:35:17: 13000000 INFO @ Sun, 21 Jun 2020 20:35:18: 8000000 INFO @ Sun, 21 Jun 2020 20:35:22: 17000000 INFO @ Sun, 21 Jun 2020 20:35:23: 14000000 INFO @ Sun, 21 Jun 2020 20:35:24: 9000000 INFO @ Sun, 21 Jun 2020 20:35:28: 18000000 INFO @ Sun, 21 Jun 2020 20:35:28: 15000000 INFO @ Sun, 21 Jun 2020 20:35:29: 10000000 INFO @ Sun, 21 Jun 2020 20:35:34: 16000000 INFO @ Sun, 21 Jun 2020 20:35:34: 19000000 INFO @ Sun, 21 Jun 2020 20:35:35: 11000000 INFO @ Sun, 21 Jun 2020 20:35:40: 17000000 INFO @ Sun, 21 Jun 2020 20:35:41: 12000000 INFO @ Sun, 21 Jun 2020 20:35:41: 20000000 INFO @ Sun, 21 Jun 2020 20:35:45: 18000000 INFO @ Sun, 21 Jun 2020 20:35:47: 13000000 INFO @ Sun, 21 Jun 2020 20:35:48: 21000000 INFO @ Sun, 21 Jun 2020 20:35:51: 19000000 INFO @ Sun, 21 Jun 2020 20:35:52: 14000000 INFO @ Sun, 21 Jun 2020 20:35:54: 22000000 INFO @ Sun, 21 Jun 2020 20:35:57: 20000000 INFO @ Sun, 21 Jun 2020 20:35:58: 15000000 INFO @ Sun, 21 Jun 2020 20:36:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:36:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:36:01: #1 total tags in treatment: 22903892 INFO @ Sun, 21 Jun 2020 20:36:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:01: #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 20:36:01: #1 tags after filtering in treatment: 22903834 INFO @ Sun, 21 Jun 2020 20:36:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:03: 21000000 INFO @ Sun, 21 Jun 2020 20:36:03: #2 number of paired peaks: 584 WARNING @ Sun, 21 Jun 2020 20:36:03: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 21 Jun 2020 20:36:03: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:03: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:03: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:03: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:03: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:36:03: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 20:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.05_model.r WARNING @ Sun, 21 Jun 2020 20:36:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:36:03: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 20:36:03: #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 20:36:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:04: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:36:08: 22000000 INFO @ Sun, 21 Jun 2020 20:36:09: 17000000 INFO @ Sun, 21 Jun 2020 20:36:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:36:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:36:13: #1 total tags in treatment: 22903892 INFO @ Sun, 21 Jun 2020 20:36:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:13: #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 20:36:14: #1 tags after filtering in treatment: 22903834 INFO @ Sun, 21 Jun 2020 20:36:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:14: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:15: 18000000 INFO @ Sun, 21 Jun 2020 20:36:15: #2 number of paired peaks: 584 WARNING @ Sun, 21 Jun 2020 20:36:15: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 21 Jun 2020 20:36:15: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:16: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:16: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:16: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:16: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:36:16: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 20:36:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.10_model.r WARNING @ Sun, 21 Jun 2020 20:36:16: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:36:16: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 20:36:16: #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 20:36:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:20: 19000000 INFO @ Sun, 21 Jun 2020 20:36:25: 20000000 INFO @ Sun, 21 Jun 2020 20:36:31: 21000000 INFO @ Sun, 21 Jun 2020 20:36:36: 22000000 INFO @ Sun, 21 Jun 2020 20:36:40: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:36:40: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:36:40: #1 total tags in treatment: 22903892 INFO @ Sun, 21 Jun 2020 20:36:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:40: #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 20:36:41: #1 tags after filtering in treatment: 22903834 INFO @ Sun, 21 Jun 2020 20:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:41: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:42: #2 number of paired peaks: 584 WARNING @ Sun, 21 Jun 2020 20:36:42: Fewer paired peaks (584) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 584 pairs to build model! INFO @ Sun, 21 Jun 2020 20:36:42: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:43: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 20:36:43: #2 alternative fragment length(s) may be 2,51 bps INFO @ Sun, 21 Jun 2020 20:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.20_model.r WARNING @ Sun, 21 Jun 2020 20:36:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:36:43: #2 You may need to consider one of the other alternative d(s): 2,51 WARNING @ Sun, 21 Jun 2020 20:36:43: #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 20:36:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:36:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:37:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.05_summits.bed INFO @ Sun, 21 Jun 2020 20:37:08: Done! pass1 - making usageList (656 chroms): 1 millis pass2 - checking and writing primary data (3660 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.10_summits.bed INFO @ Sun, 21 Jun 2020 20:37:19: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (2371 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981705/SRX3981705.20_summits.bed INFO @ Sun, 21 Jun 2020 20:37:43: Done! pass1 - making usageList (360 chroms): 2 millis pass2 - checking and writing primary data (920 records, 4 fields): 11 millis CompletedMACS2peakCalling