Job ID = 6498665 SRX = SRX681817 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:50:18 prefetch.2.10.7: 1) Downloading 'SRR1552286'... 2020-06-25T23:50:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:12:17 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:12:17 prefetch.2.10.7: 1) 'SRR1552286' was downloaded successfully Read 195883261 spots for SRR1552286/SRR1552286.sra Written 195883261 spots for SRR1552286/SRR1552286.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: 00:54:27 195883261 reads; of these: 195883261 (100.00%) were unpaired; of these: 29023319 (14.82%) aligned 0 times 149578879 (76.36%) aligned exactly 1 time 17281063 (8.82%) aligned >1 times 85.18% overall alignment rate Time searching: 00:54:27 Overall time: 00:54:27 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 68 files... [bam_rmdupse_core] 125505063 / 166859942 = 0.7522 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 @ Fri, 26 Jun 2020 10:58:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.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 @ Fri, 26 Jun 2020 10:58:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:58:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:58:07: 1000000 INFO @ Fri, 26 Jun 2020 10:58:14: 2000000 INFO @ Fri, 26 Jun 2020 10:58:20: 3000000 INFO @ Fri, 26 Jun 2020 10:58:27: 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 @ Fri, 26 Jun 2020 10:58:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.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 @ Fri, 26 Jun 2020 10:58:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:58:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:58:34: 5000000 INFO @ Fri, 26 Jun 2020 10:58:36: 1000000 INFO @ Fri, 26 Jun 2020 10:58:41: 6000000 INFO @ Fri, 26 Jun 2020 10:58:42: 2000000 INFO @ Fri, 26 Jun 2020 10:58:48: 7000000 INFO @ Fri, 26 Jun 2020 10:58:49: 3000000 INFO @ Fri, 26 Jun 2020 10:58:55: 4000000 INFO @ Fri, 26 Jun 2020 10:58:55: 8000000 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 @ Fri, 26 Jun 2020 10:59:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.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 @ Fri, 26 Jun 2020 10:59:00: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:59:00: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:59:01: 5000000 INFO @ Fri, 26 Jun 2020 10:59:02: 9000000 INFO @ Fri, 26 Jun 2020 10:59:07: 1000000 INFO @ Fri, 26 Jun 2020 10:59:08: 6000000 INFO @ Fri, 26 Jun 2020 10:59:09: 10000000 INFO @ Fri, 26 Jun 2020 10:59:14: 7000000 INFO @ Fri, 26 Jun 2020 10:59:15: 2000000 INFO @ Fri, 26 Jun 2020 10:59:16: 11000000 INFO @ Fri, 26 Jun 2020 10:59:21: 8000000 INFO @ Fri, 26 Jun 2020 10:59:22: 3000000 INFO @ Fri, 26 Jun 2020 10:59:22: 12000000 INFO @ Fri, 26 Jun 2020 10:59:27: 9000000 INFO @ Fri, 26 Jun 2020 10:59:29: 13000000 INFO @ Fri, 26 Jun 2020 10:59:30: 4000000 INFO @ Fri, 26 Jun 2020 10:59:34: 10000000 INFO @ Fri, 26 Jun 2020 10:59:36: 14000000 INFO @ Fri, 26 Jun 2020 10:59:37: 5000000 INFO @ Fri, 26 Jun 2020 10:59:41: 11000000 INFO @ Fri, 26 Jun 2020 10:59:43: 15000000 INFO @ Fri, 26 Jun 2020 10:59:44: 6000000 INFO @ Fri, 26 Jun 2020 10:59:47: 12000000 INFO @ Fri, 26 Jun 2020 10:59:49: 16000000 INFO @ Fri, 26 Jun 2020 10:59:52: 7000000 INFO @ Fri, 26 Jun 2020 10:59:53: 13000000 INFO @ Fri, 26 Jun 2020 10:59:56: 17000000 INFO @ Fri, 26 Jun 2020 10:59:59: 8000000 INFO @ Fri, 26 Jun 2020 11:00:00: 14000000 INFO @ Fri, 26 Jun 2020 11:00:03: 18000000 INFO @ Fri, 26 Jun 2020 11:00:06: 15000000 INFO @ Fri, 26 Jun 2020 11:00:06: 9000000 INFO @ Fri, 26 Jun 2020 11:00:10: 19000000 INFO @ Fri, 26 Jun 2020 11:00:12: 16000000 INFO @ Fri, 26 Jun 2020 11:00:14: 10000000 INFO @ Fri, 26 Jun 2020 11:00:17: 20000000 INFO @ Fri, 26 Jun 2020 11:00:18: 17000000 INFO @ Fri, 26 Jun 2020 11:00:21: 11000000 INFO @ Fri, 26 Jun 2020 11:00:24: 21000000 INFO @ Fri, 26 Jun 2020 11:00:25: 18000000 INFO @ Fri, 26 Jun 2020 11:00:28: 12000000 INFO @ Fri, 26 Jun 2020 11:00:31: 22000000 INFO @ Fri, 26 Jun 2020 11:00:31: 19000000 INFO @ Fri, 26 Jun 2020 11:00:35: 13000000 INFO @ Fri, 26 Jun 2020 11:00:37: 20000000 INFO @ Fri, 26 Jun 2020 11:00:38: 23000000 INFO @ Fri, 26 Jun 2020 11:00:42: 14000000 INFO @ Fri, 26 Jun 2020 11:00:43: 21000000 INFO @ Fri, 26 Jun 2020 11:00:45: 24000000 INFO @ Fri, 26 Jun 2020 11:00:49: 15000000 INFO @ Fri, 26 Jun 2020 11:00:49: 22000000 INFO @ Fri, 26 Jun 2020 11:00:51: 25000000 INFO @ Fri, 26 Jun 2020 11:00:55: 23000000 INFO @ Fri, 26 Jun 2020 11:00:55: 16000000 INFO @ Fri, 26 Jun 2020 11:00:58: 26000000 INFO @ Fri, 26 Jun 2020 11:01:01: 24000000 INFO @ Fri, 26 Jun 2020 11:01:02: 17000000 INFO @ Fri, 26 Jun 2020 11:01:05: 27000000 INFO @ Fri, 26 Jun 2020 11:01:07: 25000000 INFO @ Fri, 26 Jun 2020 11:01:09: 18000000 INFO @ Fri, 26 Jun 2020 11:01:12: 28000000 INFO @ Fri, 26 Jun 2020 11:01:13: 26000000 INFO @ Fri, 26 Jun 2020 11:01:16: 19000000 INFO @ Fri, 26 Jun 2020 11:01:18: 29000000 INFO @ Fri, 26 Jun 2020 11:01:19: 27000000 INFO @ Fri, 26 Jun 2020 11:01:23: 20000000 INFO @ Fri, 26 Jun 2020 11:01:25: 28000000 INFO @ Fri, 26 Jun 2020 11:01:25: 30000000 INFO @ Fri, 26 Jun 2020 11:01:30: 21000000 INFO @ Fri, 26 Jun 2020 11:01:31: 29000000 INFO @ Fri, 26 Jun 2020 11:01:32: 31000000 INFO @ Fri, 26 Jun 2020 11:01:37: 30000000 INFO @ Fri, 26 Jun 2020 11:01:37: 22000000 INFO @ Fri, 26 Jun 2020 11:01:39: 32000000 INFO @ Fri, 26 Jun 2020 11:01:44: 31000000 INFO @ Fri, 26 Jun 2020 11:01:44: 23000000 INFO @ Fri, 26 Jun 2020 11:01:46: 33000000 INFO @ Fri, 26 Jun 2020 11:01:50: 32000000 INFO @ Fri, 26 Jun 2020 11:01:51: 24000000 INFO @ Fri, 26 Jun 2020 11:01:53: 34000000 INFO @ Fri, 26 Jun 2020 11:01:56: 33000000 INFO @ Fri, 26 Jun 2020 11:01:58: 25000000 INFO @ Fri, 26 Jun 2020 11:02:00: 35000000 INFO @ Fri, 26 Jun 2020 11:02:02: 34000000 INFO @ Fri, 26 Jun 2020 11:02:05: 26000000 INFO @ Fri, 26 Jun 2020 11:02:07: 36000000 INFO @ Fri, 26 Jun 2020 11:02:08: 35000000 INFO @ Fri, 26 Jun 2020 11:02:12: 27000000 INFO @ Fri, 26 Jun 2020 11:02:13: 37000000 INFO @ Fri, 26 Jun 2020 11:02:14: 36000000 INFO @ Fri, 26 Jun 2020 11:02:18: 28000000 INFO @ Fri, 26 Jun 2020 11:02:20: 37000000 INFO @ Fri, 26 Jun 2020 11:02:20: 38000000 INFO @ Fri, 26 Jun 2020 11:02:25: 29000000 INFO @ Fri, 26 Jun 2020 11:02:26: 38000000 INFO @ Fri, 26 Jun 2020 11:02:27: 39000000 INFO @ Fri, 26 Jun 2020 11:02:32: 39000000 INFO @ Fri, 26 Jun 2020 11:02:32: 30000000 INFO @ Fri, 26 Jun 2020 11:02:34: 40000000 INFO @ Fri, 26 Jun 2020 11:02:38: 40000000 INFO @ Fri, 26 Jun 2020 11:02:39: 31000000 INFO @ Fri, 26 Jun 2020 11:02:41: 41000000 INFO @ Fri, 26 Jun 2020 11:02:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 11:02:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 11:02:44: #1 total tags in treatment: 41354879 INFO @ Fri, 26 Jun 2020 11:02:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:02:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 11:02:44: 41000000 INFO @ Fri, 26 Jun 2020 11:02:44: #1 tags after filtering in treatment: 41354879 INFO @ Fri, 26 Jun 2020 11:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:02:44: #1 finished! INFO @ Fri, 26 Jun 2020 11:02:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:02:46: 32000000 INFO @ Fri, 26 Jun 2020 11:02:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 11:02:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 11:02:46: #1 total tags in treatment: 41354879 INFO @ Fri, 26 Jun 2020 11:02:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:02:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 11:02:47: #1 tags after filtering in treatment: 41354879 INFO @ Fri, 26 Jun 2020 11:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:02:47: #1 finished! INFO @ Fri, 26 Jun 2020 11:02:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:02:47: #2 number of paired peaks: 143 WARNING @ Fri, 26 Jun 2020 11:02:47: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 26 Jun 2020 11:02:47: start model_add_line... INFO @ Fri, 26 Jun 2020 11:02:48: start X-correlation... INFO @ Fri, 26 Jun 2020 11:02:48: end of X-cor INFO @ Fri, 26 Jun 2020 11:02:48: #2 finished! INFO @ Fri, 26 Jun 2020 11:02:48: #2 predicted fragment length is 81 bps INFO @ Fri, 26 Jun 2020 11:02:48: #2 alternative fragment length(s) may be 4,81 bps INFO @ Fri, 26 Jun 2020 11:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.05_model.r WARNING @ Fri, 26 Jun 2020 11:02:48: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 11:02:48: #2 You may need to consider one of the other alternative d(s): 4,81 WARNING @ Fri, 26 Jun 2020 11:02:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 11:02:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:02:50: #2 number of paired peaks: 143 WARNING @ Fri, 26 Jun 2020 11:02:50: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 26 Jun 2020 11:02:50: start model_add_line... INFO @ Fri, 26 Jun 2020 11:02:50: start X-correlation... INFO @ Fri, 26 Jun 2020 11:02:50: end of X-cor INFO @ Fri, 26 Jun 2020 11:02:50: #2 finished! INFO @ Fri, 26 Jun 2020 11:02:50: #2 predicted fragment length is 81 bps INFO @ Fri, 26 Jun 2020 11:02:50: #2 alternative fragment length(s) may be 4,81 bps INFO @ Fri, 26 Jun 2020 11:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.10_model.r WARNING @ Fri, 26 Jun 2020 11:02:50: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 11:02:50: #2 You may need to consider one of the other alternative d(s): 4,81 WARNING @ Fri, 26 Jun 2020 11:02:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 11:02:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:02:52: 33000000 INFO @ Fri, 26 Jun 2020 11:02:59: 34000000 INFO @ Fri, 26 Jun 2020 11:03:05: 35000000 INFO @ Fri, 26 Jun 2020 11:03:12: 36000000 INFO @ Fri, 26 Jun 2020 11:03:18: 37000000 INFO @ Fri, 26 Jun 2020 11:03:25: 38000000 INFO @ Fri, 26 Jun 2020 11:03:32: 39000000 INFO @ Fri, 26 Jun 2020 11:03:38: 40000000 INFO @ Fri, 26 Jun 2020 11:03:45: 41000000 INFO @ Fri, 26 Jun 2020 11:03:48: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 11:03:48: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 11:03:48: #1 total tags in treatment: 41354879 INFO @ Fri, 26 Jun 2020 11:03:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 11:03:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 11:03:49: #1 tags after filtering in treatment: 41354879 INFO @ Fri, 26 Jun 2020 11:03:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 11:03:49: #1 finished! INFO @ Fri, 26 Jun 2020 11:03:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 11:03:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 11:03:52: #2 number of paired peaks: 143 WARNING @ Fri, 26 Jun 2020 11:03:52: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Fri, 26 Jun 2020 11:03:52: start model_add_line... INFO @ Fri, 26 Jun 2020 11:03:52: start X-correlation... INFO @ Fri, 26 Jun 2020 11:03:52: end of X-cor INFO @ Fri, 26 Jun 2020 11:03:52: #2 finished! INFO @ Fri, 26 Jun 2020 11:03:52: #2 predicted fragment length is 81 bps INFO @ Fri, 26 Jun 2020 11:03:52: #2 alternative fragment length(s) may be 4,81 bps INFO @ Fri, 26 Jun 2020 11:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.20_model.r WARNING @ Fri, 26 Jun 2020 11:03:52: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 11:03:52: #2 You may need to consider one of the other alternative d(s): 4,81 WARNING @ Fri, 26 Jun 2020 11:03:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 11:03:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 11:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 11:04:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:04:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 11:04:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.05_peaks.xls INFO @ Fri, 26 Jun 2020 11:04:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:04:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.05_summits.bed INFO @ Fri, 26 Jun 2020 11:04:48: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (20659 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:04:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.10_peaks.xls INFO @ Fri, 26 Jun 2020 11:04:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:04:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.10_summits.bed INFO @ Fri, 26 Jun 2020 11:04:50: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12433 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 11:05:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 11:05:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.20_peaks.xls INFO @ Fri, 26 Jun 2020 11:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 11:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681817/SRX681817.20_summits.bed INFO @ Fri, 26 Jun 2020 11:05:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5792 records, 4 fields): 10 millis CompletedMACS2peakCalling