Job ID = 6452289 SRX = ERX3548058 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:43:39 prefetch.2.10.7: 1) Downloading 'ERR3528435'... 2020-06-21T07:43:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:45:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:45:08 prefetch.2.10.7: 'ERR3528435' is valid 2020-06-21T07:45:08 prefetch.2.10.7: 1) 'ERR3528435' was downloaded successfully Read 14075858 spots for ERR3528435/ERR3528435.sra Written 14075858 spots for ERR3528435/ERR3528435.sra 2020-06-21T07:46:02 prefetch.2.10.7: 1) Downloading 'ERR3528436'... 2020-06-21T07:46:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:52:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:52:43 prefetch.2.10.7: 'ERR3528436' is valid 2020-06-21T07:52:43 prefetch.2.10.7: 1) 'ERR3528436' was downloaded successfully Read 13930464 spots for ERR3528436/ERR3528436.sra Written 13930464 spots for ERR3528436/ERR3528436.sra 2020-06-21T07:53:38 prefetch.2.10.7: 1) Downloading 'ERR3528437'... 2020-06-21T07:53:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:55:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:55:48 prefetch.2.10.7: 'ERR3528437' is valid 2020-06-21T07:55:48 prefetch.2.10.7: 1) 'ERR3528437' was downloaded successfully Read 14125279 spots for ERR3528437/ERR3528437.sra Written 14125279 spots for ERR3528437/ERR3528437.sra 2020-06-21T07:56:45 prefetch.2.10.7: 1) Downloading 'ERR3528438'... 2020-06-21T07:56:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:58:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:58:08 prefetch.2.10.7: 'ERR3528438' is valid 2020-06-21T07:58:08 prefetch.2.10.7: 1) 'ERR3528438' was downloaded successfully Read 13865010 spots for ERR3528438/ERR3528438.sra Written 13865010 spots for ERR3528438/ERR3528438.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: 00:00:01 Multiseed full-index search: 00:15:12 55996611 reads; of these: 55996611 (100.00%) were unpaired; of these: 1814989 (3.24%) aligned 0 times 38869609 (69.41%) aligned exactly 1 time 15312013 (27.34%) aligned >1 times 96.76% overall alignment rate Time searching: 00:15:13 Overall time: 00:15:13 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 24 files... [bam_rmdupse_core] 25327482 / 54181622 = 0.4675 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 17:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.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 17:23:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:10: 1000000 INFO @ Sun, 21 Jun 2020 17:23:16: 2000000 INFO @ Sun, 21 Jun 2020 17:23:23: 3000000 INFO @ Sun, 21 Jun 2020 17:23:30: 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 17:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.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 17:23:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:37: 5000000 INFO @ Sun, 21 Jun 2020 17:23:40: 1000000 INFO @ Sun, 21 Jun 2020 17:23:44: 6000000 INFO @ Sun, 21 Jun 2020 17:23:48: 2000000 INFO @ Sun, 21 Jun 2020 17:23:51: 7000000 INFO @ Sun, 21 Jun 2020 17:23:56: 3000000 INFO @ Sun, 21 Jun 2020 17:23:59: 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 @ Sun, 21 Jun 2020 17:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.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 17:24:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:03: 4000000 INFO @ Sun, 21 Jun 2020 17:24:06: 9000000 INFO @ Sun, 21 Jun 2020 17:24:11: 5000000 INFO @ Sun, 21 Jun 2020 17:24:11: 1000000 INFO @ Sun, 21 Jun 2020 17:24:14: 10000000 INFO @ Sun, 21 Jun 2020 17:24:19: 6000000 INFO @ Sun, 21 Jun 2020 17:24:19: 2000000 INFO @ Sun, 21 Jun 2020 17:24:21: 11000000 INFO @ Sun, 21 Jun 2020 17:24:26: 7000000 INFO @ Sun, 21 Jun 2020 17:24:27: 3000000 INFO @ Sun, 21 Jun 2020 17:24:29: 12000000 INFO @ Sun, 21 Jun 2020 17:24:34: 8000000 INFO @ Sun, 21 Jun 2020 17:24:35: 4000000 INFO @ Sun, 21 Jun 2020 17:24:36: 13000000 INFO @ Sun, 21 Jun 2020 17:24:42: 9000000 INFO @ Sun, 21 Jun 2020 17:24:43: 5000000 INFO @ Sun, 21 Jun 2020 17:24:44: 14000000 INFO @ Sun, 21 Jun 2020 17:24:49: 10000000 INFO @ Sun, 21 Jun 2020 17:24:50: 6000000 INFO @ Sun, 21 Jun 2020 17:24:51: 15000000 INFO @ Sun, 21 Jun 2020 17:24:57: 11000000 INFO @ Sun, 21 Jun 2020 17:24:58: 7000000 INFO @ Sun, 21 Jun 2020 17:24:59: 16000000 INFO @ Sun, 21 Jun 2020 17:25:05: 12000000 INFO @ Sun, 21 Jun 2020 17:25:06: 8000000 INFO @ Sun, 21 Jun 2020 17:25:06: 17000000 INFO @ Sun, 21 Jun 2020 17:25:12: 13000000 INFO @ Sun, 21 Jun 2020 17:25:14: 18000000 INFO @ Sun, 21 Jun 2020 17:25:14: 9000000 INFO @ Sun, 21 Jun 2020 17:25:20: 14000000 INFO @ Sun, 21 Jun 2020 17:25:21: 19000000 INFO @ Sun, 21 Jun 2020 17:25:22: 10000000 INFO @ Sun, 21 Jun 2020 17:25:28: 15000000 INFO @ Sun, 21 Jun 2020 17:25:29: 20000000 INFO @ Sun, 21 Jun 2020 17:25:30: 11000000 INFO @ Sun, 21 Jun 2020 17:25:35: 16000000 INFO @ Sun, 21 Jun 2020 17:25:36: 21000000 INFO @ Sun, 21 Jun 2020 17:25:37: 12000000 INFO @ Sun, 21 Jun 2020 17:25:43: 17000000 INFO @ Sun, 21 Jun 2020 17:25:43: 22000000 INFO @ Sun, 21 Jun 2020 17:25:45: 13000000 INFO @ Sun, 21 Jun 2020 17:25:51: 18000000 INFO @ Sun, 21 Jun 2020 17:25:51: 23000000 INFO @ Sun, 21 Jun 2020 17:25:53: 14000000 INFO @ Sun, 21 Jun 2020 17:25:58: 19000000 INFO @ Sun, 21 Jun 2020 17:25:58: 24000000 INFO @ Sun, 21 Jun 2020 17:26:01: 15000000 INFO @ Sun, 21 Jun 2020 17:26:06: 20000000 INFO @ Sun, 21 Jun 2020 17:26:06: 25000000 INFO @ Sun, 21 Jun 2020 17:26:09: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:26:14: 21000000 INFO @ Sun, 21 Jun 2020 17:26:14: 26000000 INFO @ Sun, 21 Jun 2020 17:26:17: 17000000 INFO @ Sun, 21 Jun 2020 17:26:21: 22000000 INFO @ Sun, 21 Jun 2020 17:26:22: 27000000 INFO @ Sun, 21 Jun 2020 17:26:25: 18000000 INFO @ Sun, 21 Jun 2020 17:26:29: 23000000 INFO @ Sun, 21 Jun 2020 17:26:30: 28000000 INFO @ Sun, 21 Jun 2020 17:26:33: 19000000 INFO @ Sun, 21 Jun 2020 17:26:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:26:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:26:36: #1 total tags in treatment: 28854140 INFO @ Sun, 21 Jun 2020 17:26:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:36: #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 17:26:37: 24000000 INFO @ Sun, 21 Jun 2020 17:26:37: #1 tags after filtering in treatment: 28854087 INFO @ Sun, 21 Jun 2020 17:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:39: #2 number of paired peaks: 1268 INFO @ Sun, 21 Jun 2020 17:26:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:39: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:26:39: #2 alternative fragment length(s) may be 1,67,124 bps INFO @ Sun, 21 Jun 2020 17:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.05_model.r WARNING @ Sun, 21 Jun 2020 17:26:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:26:39: #2 You may need to consider one of the other alternative d(s): 1,67,124 WARNING @ Sun, 21 Jun 2020 17:26:39: #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 17:26:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:26:40: 20000000 INFO @ Sun, 21 Jun 2020 17:26:44: 25000000 INFO @ Sun, 21 Jun 2020 17:26:48: 21000000 INFO @ Sun, 21 Jun 2020 17:26:52: 26000000 INFO @ Sun, 21 Jun 2020 17:26:56: 22000000 INFO @ Sun, 21 Jun 2020 17:27:00: 27000000 INFO @ Sun, 21 Jun 2020 17:27:03: 23000000 INFO @ Sun, 21 Jun 2020 17:27:07: 28000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:27:11: 24000000 INFO @ Sun, 21 Jun 2020 17:27:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:27:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:27:14: #1 total tags in treatment: 28854140 INFO @ Sun, 21 Jun 2020 17:27:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:14: #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 17:27:15: #1 tags after filtering in treatment: 28854087 INFO @ Sun, 21 Jun 2020 17:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:15: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:27:17: #2 number of paired peaks: 1268 INFO @ Sun, 21 Jun 2020 17:27:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:17: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:27:17: #2 alternative fragment length(s) may be 1,67,124 bps INFO @ Sun, 21 Jun 2020 17:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.10_model.r WARNING @ Sun, 21 Jun 2020 17:27:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:27:17: #2 You may need to consider one of the other alternative d(s): 1,67,124 WARNING @ Sun, 21 Jun 2020 17:27:17: #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 17:27:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:27:19: 25000000 INFO @ Sun, 21 Jun 2020 17:27:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:26: 26000000 INFO @ Sun, 21 Jun 2020 17:27:33: 27000000 INFO @ Sun, 21 Jun 2020 17:27:40: 28000000 INFO @ Sun, 21 Jun 2020 17:27:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.05_summits.bed INFO @ Sun, 21 Jun 2020 17:27:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:27:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:27:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:27:46: #1 total tags in treatment: 28854140 INFO @ Sun, 21 Jun 2020 17:27:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:27:46: #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 17:27:47: #1 tags after filtering in treatment: 28854087 INFO @ Sun, 21 Jun 2020 17:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:27:47: #1 finished! INFO @ Sun, 21 Jun 2020 17:27:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:27:49: #2 number of paired peaks: 1268 INFO @ Sun, 21 Jun 2020 17:27:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:27:49: start X-correlation... INFO @ Sun, 21 Jun 2020 17:27:49: end of X-cor INFO @ Sun, 21 Jun 2020 17:27:49: #2 finished! INFO @ Sun, 21 Jun 2020 17:27:49: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 17:27:49: #2 alternative fragment length(s) may be 1,67,124 bps INFO @ Sun, 21 Jun 2020 17:27:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.20_model.r WARNING @ Sun, 21 Jun 2020 17:27:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:27:49: #2 You may need to consider one of the other alternative d(s): 1,67,124 WARNING @ Sun, 21 Jun 2020 17:27:49: #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 17:27:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:27:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.10_summits.bed INFO @ Sun, 21 Jun 2020 17:28:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:28:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:28:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:28:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:28:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX3548058/ERX3548058.20_summits.bed INFO @ Sun, 21 Jun 2020 17:28:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling