Job ID = 6527854 SRX = SRX287878 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:42:15 prefetch.2.10.7: 1) Downloading 'SRR870067'... 2020-06-29T13:42:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:52:56 prefetch.2.10.7: HTTPS download failed 2020-06-29T13:52:56 prefetch.2.10.7: 1) failed to download SRR870067 2020-06-29T13:53:09 prefetch.2.10.7: 1) Downloading 'SRR870067'... 2020-06-29T13:53:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:53:09 prefetch.2.10.7: Continue download of 'SRR870067' from 877975777 2020-06-29T13:53:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:53:14 prefetch.2.10.7: 1) 'SRR870067' was downloaded successfully Read 26274958 spots for SRR870067/SRR870067.sra Written 26274958 spots for SRR870067/SRR870067.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:11 26274958 reads; of these: 26274958 (100.00%) were unpaired; of these: 1296651 (4.93%) aligned 0 times 16585689 (63.12%) aligned exactly 1 time 8392618 (31.94%) aligned >1 times 95.07% overall alignment rate Time searching: 00:09:12 Overall time: 00:09:12 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] 4734221 / 24978307 = 0.1895 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 23:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.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 23:15:30: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:15:30: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:15:35: 1000000 INFO @ Mon, 29 Jun 2020 23:15:41: 2000000 INFO @ Mon, 29 Jun 2020 23:15:46: 3000000 INFO @ Mon, 29 Jun 2020 23:15:51: 4000000 INFO @ Mon, 29 Jun 2020 23:15:57: 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 23:15:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.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 23:15:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:15:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:16:02: 6000000 INFO @ Mon, 29 Jun 2020 23:16:06: 1000000 INFO @ Mon, 29 Jun 2020 23:16:09: 7000000 INFO @ Mon, 29 Jun 2020 23:16:14: 2000000 INFO @ Mon, 29 Jun 2020 23:16:15: 8000000 INFO @ Mon, 29 Jun 2020 23:16:21: 3000000 INFO @ Mon, 29 Jun 2020 23:16:21: 9000000 INFO @ Mon, 29 Jun 2020 23:16:27: 10000000 INFO @ Mon, 29 Jun 2020 23:16:27: 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 @ Mon, 29 Jun 2020 23:16:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.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 23:16:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:16:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:16:34: 11000000 INFO @ Mon, 29 Jun 2020 23:16:34: 5000000 INFO @ Mon, 29 Jun 2020 23:16:36: 1000000 INFO @ Mon, 29 Jun 2020 23:16:40: 12000000 INFO @ Mon, 29 Jun 2020 23:16:41: 6000000 INFO @ Mon, 29 Jun 2020 23:16:43: 2000000 INFO @ Mon, 29 Jun 2020 23:16:47: 13000000 INFO @ Mon, 29 Jun 2020 23:16:48: 7000000 INFO @ Mon, 29 Jun 2020 23:16:49: 3000000 INFO @ Mon, 29 Jun 2020 23:16:53: 14000000 INFO @ Mon, 29 Jun 2020 23:16:55: 8000000 INFO @ Mon, 29 Jun 2020 23:16:56: 4000000 INFO @ Mon, 29 Jun 2020 23:17:00: 15000000 INFO @ Mon, 29 Jun 2020 23:17:02: 9000000 INFO @ Mon, 29 Jun 2020 23:17:02: 5000000 INFO @ Mon, 29 Jun 2020 23:17:06: 16000000 INFO @ Mon, 29 Jun 2020 23:17:09: 6000000 INFO @ Mon, 29 Jun 2020 23:17:09: 10000000 INFO @ Mon, 29 Jun 2020 23:17:13: 17000000 INFO @ Mon, 29 Jun 2020 23:17:15: 7000000 INFO @ Mon, 29 Jun 2020 23:17:16: 11000000 INFO @ Mon, 29 Jun 2020 23:17:19: 18000000 INFO @ Mon, 29 Jun 2020 23:17:21: 8000000 INFO @ Mon, 29 Jun 2020 23:17:23: 12000000 INFO @ Mon, 29 Jun 2020 23:17:26: 19000000 INFO @ Mon, 29 Jun 2020 23:17:28: 9000000 INFO @ Mon, 29 Jun 2020 23:17:31: 13000000 INFO @ Mon, 29 Jun 2020 23:17:32: 20000000 INFO @ Mon, 29 Jun 2020 23:17:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:17:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:17:34: #1 total tags in treatment: 20244086 INFO @ Mon, 29 Jun 2020 23:17:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:17:34: #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 23:17:34: #1 tags after filtering in treatment: 20244086 INFO @ Mon, 29 Jun 2020 23:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:17:34: #1 finished! INFO @ Mon, 29 Jun 2020 23:17:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:17:34: 10000000 INFO @ Mon, 29 Jun 2020 23:17:35: #2 number of paired peaks: 185 WARNING @ Mon, 29 Jun 2020 23:17:35: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Mon, 29 Jun 2020 23:17:35: start model_add_line... INFO @ Mon, 29 Jun 2020 23:17:35: start X-correlation... INFO @ Mon, 29 Jun 2020 23:17:35: end of X-cor INFO @ Mon, 29 Jun 2020 23:17:35: #2 finished! INFO @ Mon, 29 Jun 2020 23:17:35: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:17:35: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.05_model.r WARNING @ Mon, 29 Jun 2020 23:17:35: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:17:35: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:17:35: #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 23:17:35: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:17:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:17:38: 14000000 INFO @ Mon, 29 Jun 2020 23:17:41: 11000000 INFO @ Mon, 29 Jun 2020 23:17:45: 15000000 INFO @ Mon, 29 Jun 2020 23:17:47: 12000000 INFO @ Mon, 29 Jun 2020 23:17:52: 16000000 INFO @ Mon, 29 Jun 2020 23:17:54: 13000000 INFO @ Mon, 29 Jun 2020 23:17:59: 17000000 INFO @ Mon, 29 Jun 2020 23:18:00: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:18:06: 18000000 INFO @ Mon, 29 Jun 2020 23:18:06: 15000000 INFO @ Mon, 29 Jun 2020 23:18:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:18:13: 16000000 INFO @ Mon, 29 Jun 2020 23:18:13: 19000000 INFO @ Mon, 29 Jun 2020 23:18:19: 17000000 INFO @ Mon, 29 Jun 2020 23:18:19: 20000000 INFO @ Mon, 29 Jun 2020 23:18:21: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:18:21: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:18:21: #1 total tags in treatment: 20244086 INFO @ Mon, 29 Jun 2020 23:18:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:18:21: #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 23:18:22: #1 tags after filtering in treatment: 20244086 INFO @ Mon, 29 Jun 2020 23:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:18:22: #1 finished! INFO @ Mon, 29 Jun 2020 23:18:22: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:18:23: #2 number of paired peaks: 185 WARNING @ Mon, 29 Jun 2020 23:18:23: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Mon, 29 Jun 2020 23:18:23: start model_add_line... INFO @ Mon, 29 Jun 2020 23:18:23: start X-correlation... INFO @ Mon, 29 Jun 2020 23:18:23: end of X-cor INFO @ Mon, 29 Jun 2020 23:18:23: #2 finished! INFO @ Mon, 29 Jun 2020 23:18:23: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:18:23: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.10_model.r WARNING @ Mon, 29 Jun 2020 23:18:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:18:23: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:18:23: #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 23:18:23: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:18:25: 18000000 INFO @ Mon, 29 Jun 2020 23:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.05_summits.bed INFO @ Mon, 29 Jun 2020 23:18:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2263 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:18:31: 19000000 INFO @ Mon, 29 Jun 2020 23:18:37: 20000000 INFO @ Mon, 29 Jun 2020 23:18:39: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:18:39: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:18:39: #1 total tags in treatment: 20244086 INFO @ Mon, 29 Jun 2020 23:18:39: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:18:39: #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 23:18:39: #1 tags after filtering in treatment: 20244086 INFO @ Mon, 29 Jun 2020 23:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:18:39: #1 finished! INFO @ Mon, 29 Jun 2020 23:18:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:18:40: #2 number of paired peaks: 185 WARNING @ Mon, 29 Jun 2020 23:18:40: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Mon, 29 Jun 2020 23:18:40: start model_add_line... INFO @ Mon, 29 Jun 2020 23:18:40: start X-correlation... INFO @ Mon, 29 Jun 2020 23:18:40: end of X-cor INFO @ Mon, 29 Jun 2020 23:18:40: #2 finished! INFO @ Mon, 29 Jun 2020 23:18:40: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:18:40: #2 alternative fragment length(s) may be 44 bps INFO @ Mon, 29 Jun 2020 23:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.20_model.r WARNING @ Mon, 29 Jun 2020 23:18:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:18:40: #2 You may need to consider one of the other alternative d(s): 44 WARNING @ Mon, 29 Jun 2020 23:18:40: #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 23:18:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:18:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:19:00: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:19:17: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.10_summits.bed INFO @ Mon, 29 Jun 2020 23:19:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1857 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:19:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:19:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287878/SRX287878.20_summits.bed INFO @ Mon, 29 Jun 2020 23:19:35: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1430 records, 4 fields): 3 millis CompletedMACS2peakCalling