Job ID = 6527767 SRX = SRX2734368 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:23:34 prefetch.2.10.7: 1) Downloading 'SRR5445345'... 2020-06-29T13:23:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:26:37 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:26:38 prefetch.2.10.7: 'SRR5445345' is valid 2020-06-29T13:26:38 prefetch.2.10.7: 1) 'SRR5445345' was downloaded successfully 2020-06-29T13:26:38 prefetch.2.10.7: 'SRR5445345' has 0 unresolved dependencies Read 29987095 spots for SRR5445345/SRR5445345.sra Written 29987095 spots for SRR5445345/SRR5445345.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: 00:07:31 29987095 reads; of these: 29987095 (100.00%) were unpaired; of these: 1585191 (5.29%) aligned 0 times 23671795 (78.94%) aligned exactly 1 time 4730109 (15.77%) aligned >1 times 94.71% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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 12 files... [bam_rmdupse_core] 3647152 / 28401904 = 0.1284 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 @ Mon, 29 Jun 2020 22:47:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.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 @ Mon, 29 Jun 2020 22:47:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:47:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:47:15: 1000000 INFO @ Mon, 29 Jun 2020 22:47:20: 2000000 INFO @ Mon, 29 Jun 2020 22:47:25: 3000000 INFO @ Mon, 29 Jun 2020 22:47:30: 4000000 INFO @ Mon, 29 Jun 2020 22:47:34: 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 @ Mon, 29 Jun 2020 22:47:39: 6000000 INFO @ Mon, 29 Jun 2020 22:47:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.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 @ Mon, 29 Jun 2020 22:47:41: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:47:41: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:47:44: 7000000 INFO @ Mon, 29 Jun 2020 22:47:46: 1000000 INFO @ Mon, 29 Jun 2020 22:47:49: 8000000 INFO @ Mon, 29 Jun 2020 22:47:51: 2000000 INFO @ Mon, 29 Jun 2020 22:47:54: 9000000 INFO @ Mon, 29 Jun 2020 22:47:56: 3000000 INFO @ Mon, 29 Jun 2020 22:47:59: 10000000 INFO @ Mon, 29 Jun 2020 22:48:01: 4000000 INFO @ Mon, 29 Jun 2020 22:48:04: 11000000 INFO @ Mon, 29 Jun 2020 22:48:06: 5000000 INFO @ Mon, 29 Jun 2020 22:48:09: 12000000 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 @ Mon, 29 Jun 2020 22:48:10: 6000000 INFO @ Mon, 29 Jun 2020 22:48:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.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 @ Mon, 29 Jun 2020 22:48:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:48:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:48:14: 13000000 INFO @ Mon, 29 Jun 2020 22:48:15: 7000000 INFO @ Mon, 29 Jun 2020 22:48:16: 1000000 INFO @ Mon, 29 Jun 2020 22:48:19: 14000000 INFO @ Mon, 29 Jun 2020 22:48:21: 8000000 INFO @ Mon, 29 Jun 2020 22:48:21: 2000000 INFO @ Mon, 29 Jun 2020 22:48:24: 15000000 INFO @ Mon, 29 Jun 2020 22:48:25: 9000000 INFO @ Mon, 29 Jun 2020 22:48:26: 3000000 INFO @ Mon, 29 Jun 2020 22:48:29: 16000000 INFO @ Mon, 29 Jun 2020 22:48:30: 10000000 INFO @ Mon, 29 Jun 2020 22:48:31: 4000000 INFO @ Mon, 29 Jun 2020 22:48:34: 17000000 INFO @ Mon, 29 Jun 2020 22:48:35: 11000000 INFO @ Mon, 29 Jun 2020 22:48:37: 5000000 INFO @ Mon, 29 Jun 2020 22:48:39: 18000000 INFO @ Mon, 29 Jun 2020 22:48:40: 12000000 INFO @ Mon, 29 Jun 2020 22:48:42: 6000000 INFO @ Mon, 29 Jun 2020 22:48:44: 19000000 INFO @ Mon, 29 Jun 2020 22:48:46: 13000000 INFO @ Mon, 29 Jun 2020 22:48:47: 7000000 INFO @ Mon, 29 Jun 2020 22:48:48: 20000000 INFO @ Mon, 29 Jun 2020 22:48:51: 14000000 INFO @ Mon, 29 Jun 2020 22:48:52: 8000000 INFO @ Mon, 29 Jun 2020 22:48:53: 21000000 INFO @ Mon, 29 Jun 2020 22:48:56: 15000000 INFO @ Mon, 29 Jun 2020 22:48:57: 9000000 INFO @ Mon, 29 Jun 2020 22:48:58: 22000000 INFO @ Mon, 29 Jun 2020 22:49:01: 16000000 INFO @ Mon, 29 Jun 2020 22:49:02: 10000000 INFO @ Mon, 29 Jun 2020 22:49:03: 23000000 INFO @ Mon, 29 Jun 2020 22:49:06: 17000000 INFO @ Mon, 29 Jun 2020 22:49:07: 11000000 INFO @ Mon, 29 Jun 2020 22:49:08: 24000000 INFO @ Mon, 29 Jun 2020 22:49:11: 18000000 INFO @ Mon, 29 Jun 2020 22:49:12: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:49:12: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:49:12: #1 total tags in treatment: 24754752 INFO @ Mon, 29 Jun 2020 22:49:12: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:49:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:49:13: 12000000 INFO @ Mon, 29 Jun 2020 22:49:13: #1 tags after filtering in treatment: 24754752 INFO @ Mon, 29 Jun 2020 22:49:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:49:13: #1 finished! INFO @ Mon, 29 Jun 2020 22:49:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:49:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:49:14: #2 number of paired peaks: 101 WARNING @ Mon, 29 Jun 2020 22:49:14: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Mon, 29 Jun 2020 22:49:14: start model_add_line... INFO @ Mon, 29 Jun 2020 22:49:14: start X-correlation... INFO @ Mon, 29 Jun 2020 22:49:14: end of X-cor INFO @ Mon, 29 Jun 2020 22:49:14: #2 finished! INFO @ Mon, 29 Jun 2020 22:49:14: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 22:49:14: #2 alternative fragment length(s) may be 2,48,79,111,126,136,448,477,527,567,593,597 bps INFO @ Mon, 29 Jun 2020 22:49:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.05_model.r WARNING @ Mon, 29 Jun 2020 22:49:14: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:49:14: #2 You may need to consider one of the other alternative d(s): 2,48,79,111,126,136,448,477,527,567,593,597 WARNING @ Mon, 29 Jun 2020 22:49:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:49:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:49:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:49:15: 19000000 INFO @ Mon, 29 Jun 2020 22:49:18: 13000000 INFO @ Mon, 29 Jun 2020 22:49:20: 20000000 INFO @ Mon, 29 Jun 2020 22:49:23: 14000000 INFO @ Mon, 29 Jun 2020 22:49:25: 21000000 INFO @ Mon, 29 Jun 2020 22:49:28: 15000000 INFO @ Mon, 29 Jun 2020 22:49:30: 22000000 INFO @ Mon, 29 Jun 2020 22:49:33: 16000000 INFO @ Mon, 29 Jun 2020 22:49:35: 23000000 INFO @ Mon, 29 Jun 2020 22:49:38: 17000000 INFO @ Mon, 29 Jun 2020 22:49:40: 24000000 INFO @ Mon, 29 Jun 2020 22:49:43: 18000000 INFO @ Mon, 29 Jun 2020 22:49:44: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:49:44: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:49:44: #1 total tags in treatment: 24754752 INFO @ Mon, 29 Jun 2020 22:49:44: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:49:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:49:44: #1 tags after filtering in treatment: 24754752 INFO @ Mon, 29 Jun 2020 22:49:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:49:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:49:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:49:46: #2 number of paired peaks: 101 WARNING @ Mon, 29 Jun 2020 22:49:46: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Mon, 29 Jun 2020 22:49:46: start model_add_line... INFO @ Mon, 29 Jun 2020 22:49:46: start X-correlation... INFO @ Mon, 29 Jun 2020 22:49:46: end of X-cor INFO @ Mon, 29 Jun 2020 22:49:46: #2 finished! INFO @ Mon, 29 Jun 2020 22:49:46: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 22:49:46: #2 alternative fragment length(s) may be 2,48,79,111,126,136,448,477,527,567,593,597 bps INFO @ Mon, 29 Jun 2020 22:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.10_model.r WARNING @ Mon, 29 Jun 2020 22:49:46: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:49:46: #2 You may need to consider one of the other alternative d(s): 2,48,79,111,126,136,448,477,527,567,593,597 WARNING @ Mon, 29 Jun 2020 22:49:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:49:46: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:49:48: 19000000 INFO @ Mon, 29 Jun 2020 22:49:52: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:49:57: 21000000 INFO @ Mon, 29 Jun 2020 22:49:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:50:02: 22000000 INFO @ Mon, 29 Jun 2020 22:50:07: 23000000 INFO @ Mon, 29 Jun 2020 22:50:11: 24000000 INFO @ Mon, 29 Jun 2020 22:50:15: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:50:15: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:50:15: #1 total tags in treatment: 24754752 INFO @ Mon, 29 Jun 2020 22:50:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:50:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:50:16: #1 tags after filtering in treatment: 24754752 INFO @ Mon, 29 Jun 2020 22:50:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:50:16: #1 finished! INFO @ Mon, 29 Jun 2020 22:50:16: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:50:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:50:17: #2 number of paired peaks: 101 WARNING @ Mon, 29 Jun 2020 22:50:17: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Mon, 29 Jun 2020 22:50:17: start model_add_line... INFO @ Mon, 29 Jun 2020 22:50:17: start X-correlation... INFO @ Mon, 29 Jun 2020 22:50:17: end of X-cor INFO @ Mon, 29 Jun 2020 22:50:17: #2 finished! INFO @ Mon, 29 Jun 2020 22:50:17: #2 predicted fragment length is 48 bps INFO @ Mon, 29 Jun 2020 22:50:17: #2 alternative fragment length(s) may be 2,48,79,111,126,136,448,477,527,567,593,597 bps INFO @ Mon, 29 Jun 2020 22:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.20_model.r WARNING @ Mon, 29 Jun 2020 22:50:17: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:50:17: #2 You may need to consider one of the other alternative d(s): 2,48,79,111,126,136,448,477,527,567,593,597 WARNING @ Mon, 29 Jun 2020 22:50:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:50:17: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.05_summits.bed INFO @ Mon, 29 Jun 2020 22:50:19: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:50:28: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:50:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:50:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:50:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.10_summits.bed INFO @ Mon, 29 Jun 2020 22:50:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:51:01: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2734368/SRX2734368.20_summits.bed INFO @ Mon, 29 Jun 2020 22:51:21: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (79 records, 4 fields): 1 millis CompletedMACS2peakCalling