Job ID = 6456323 SRX = SRX335521 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:37:59 prefetch.2.10.7: 1) Downloading 'SRR952863'... 2020-06-21T10:37:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:40:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:40:29 prefetch.2.10.7: 1) 'SRR952863' was downloaded successfully Read 17643933 spots for SRR952863/SRR952863.sra Written 17643933 spots for SRR952863/SRR952863.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: 00:05:23 17643933 reads; of these: 17643933 (100.00%) were unpaired; of these: 1075777 (6.10%) aligned 0 times 11627076 (65.90%) aligned exactly 1 time 4941080 (28.00%) aligned >1 times 93.90% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 4020382 / 16568156 = 0.2427 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 19:50:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.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 19:50:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:33: 1000000 INFO @ Sun, 21 Jun 2020 19:50:39: 2000000 INFO @ Sun, 21 Jun 2020 19:50:45: 3000000 INFO @ Sun, 21 Jun 2020 19:50:51: 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 19:50:57: 5000000 INFO @ Sun, 21 Jun 2020 19:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.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 19:50:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:03: 6000000 INFO @ Sun, 21 Jun 2020 19:51:04: 1000000 INFO @ Sun, 21 Jun 2020 19:51:09: 7000000 INFO @ Sun, 21 Jun 2020 19:51:10: 2000000 INFO @ Sun, 21 Jun 2020 19:51:15: 8000000 INFO @ Sun, 21 Jun 2020 19:51:16: 3000000 INFO @ Sun, 21 Jun 2020 19:51:21: 9000000 INFO @ Sun, 21 Jun 2020 19:51:22: 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 19:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.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 19:51:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:28: 10000000 INFO @ Sun, 21 Jun 2020 19:51:29: 5000000 INFO @ Sun, 21 Jun 2020 19:51:34: 1000000 INFO @ Sun, 21 Jun 2020 19:51:35: 11000000 INFO @ Sun, 21 Jun 2020 19:51:35: 6000000 INFO @ Sun, 21 Jun 2020 19:51:41: 2000000 INFO @ Sun, 21 Jun 2020 19:51:41: 12000000 INFO @ Sun, 21 Jun 2020 19:51:42: 7000000 INFO @ Sun, 21 Jun 2020 19:51:45: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:45: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:45: #1 total tags in treatment: 12547774 INFO @ Sun, 21 Jun 2020 19:51:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:45: #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 19:51:46: #1 tags after filtering in treatment: 12547689 INFO @ Sun, 21 Jun 2020 19:51:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:46: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:47: #2 number of paired peaks: 205 WARNING @ Sun, 21 Jun 2020 19:51:47: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 21 Jun 2020 19:51:47: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:47: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:47: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:47: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:47: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 19:51:47: #2 alternative fragment length(s) may be 2,13,59,574 bps INFO @ Sun, 21 Jun 2020 19:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.05_model.r WARNING @ Sun, 21 Jun 2020 19:51:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:51:47: #2 You may need to consider one of the other alternative d(s): 2,13,59,574 WARNING @ Sun, 21 Jun 2020 19:51:47: #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 19:51:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:48: 3000000 INFO @ Sun, 21 Jun 2020 19:51:49: 8000000 INFO @ Sun, 21 Jun 2020 19:51:54: 4000000 INFO @ Sun, 21 Jun 2020 19:51:56: 9000000 INFO @ Sun, 21 Jun 2020 19:52:01: 5000000 INFO @ Sun, 21 Jun 2020 19:52:03: 10000000 INFO @ Sun, 21 Jun 2020 19:52:07: 6000000 INFO @ Sun, 21 Jun 2020 19:52:10: 11000000 INFO @ Sun, 21 Jun 2020 19:52:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:14: 7000000 INFO @ Sun, 21 Jun 2020 19:52:16: 12000000 INFO @ Sun, 21 Jun 2020 19:52:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:52:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:52:20: #1 total tags in treatment: 12547774 INFO @ Sun, 21 Jun 2020 19:52:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:20: #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 19:52:21: 8000000 INFO @ Sun, 21 Jun 2020 19:52:21: #1 tags after filtering in treatment: 12547689 INFO @ Sun, 21 Jun 2020 19:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:22: #2 number of paired peaks: 205 WARNING @ Sun, 21 Jun 2020 19:52:22: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 21 Jun 2020 19:52:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:22: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 19:52:22: #2 alternative fragment length(s) may be 2,13,59,574 bps INFO @ Sun, 21 Jun 2020 19:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.10_model.r WARNING @ Sun, 21 Jun 2020 19:52:22: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:52:22: #2 You may need to consider one of the other alternative d(s): 2,13,59,574 WARNING @ Sun, 21 Jun 2020 19:52:22: #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 19:52:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.05_summits.bed INFO @ Sun, 21 Jun 2020 19:52:24: Done! pass1 - making usageList (543 chroms): 1 millis pass2 - checking and writing primary data (1929 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:52:27: 9000000 INFO @ Sun, 21 Jun 2020 19:52:33: 10000000 INFO @ Sun, 21 Jun 2020 19:52:39: 11000000 INFO @ Sun, 21 Jun 2020 19:52:45: 12000000 INFO @ Sun, 21 Jun 2020 19:52:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:52:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:52:48: #1 total tags in treatment: 12547774 INFO @ Sun, 21 Jun 2020 19:52:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:48: #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 19:52:49: #1 tags after filtering in treatment: 12547689 INFO @ Sun, 21 Jun 2020 19:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:49: #2 number of paired peaks: 205 WARNING @ Sun, 21 Jun 2020 19:52:49: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sun, 21 Jun 2020 19:52:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:50: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 19:52:50: #2 alternative fragment length(s) may be 2,13,59,574 bps INFO @ Sun, 21 Jun 2020 19:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.20_model.r WARNING @ Sun, 21 Jun 2020 19:52:50: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:52:50: #2 You may need to consider one of the other alternative d(s): 2,13,59,574 WARNING @ Sun, 21 Jun 2020 19:52:50: #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 19:52:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.10_summits.bed INFO @ Sun, 21 Jun 2020 19:52:59: Done! pass1 - making usageList (330 chroms): 1 millis pass2 - checking and writing primary data (770 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:53:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335521/SRX335521.20_summits.bed INFO @ Sun, 21 Jun 2020 19:53:27: Done! pass1 - making usageList (96 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 3 millis CompletedMACS2peakCalling