Job ID = 6453842 SRX = SRX152097 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:42:17 prefetch.2.10.7: 1) Downloading 'SRR504953'... 2020-06-21T08:42:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:46:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:46:28 prefetch.2.10.7: 'SRR504953' is valid 2020-06-21T08:46:28 prefetch.2.10.7: 1) 'SRR504953' was downloaded successfully Read 13356499 spots for SRR504953/SRR504953.sra Written 13356499 spots for SRR504953/SRR504953.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: 00:02:52 13356499 reads; of these: 13356499 (100.00%) were unpaired; of these: 309666 (2.32%) aligned 0 times 11652000 (87.24%) aligned exactly 1 time 1394833 (10.44%) aligned >1 times 97.68% overall alignment rate Time searching: 00:02:52 Overall time: 00:02:52 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] 4053916 / 13046833 = 0.3107 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 17:53:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.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 17:53:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:53:30: 1000000 INFO @ Sun, 21 Jun 2020 17:53:36: 2000000 INFO @ Sun, 21 Jun 2020 17:53:42: 3000000 INFO @ Sun, 21 Jun 2020 17:53:48: 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 17:53:53: 5000000 INFO @ Sun, 21 Jun 2020 17:53:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.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 17:53:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:53:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:00: 6000000 INFO @ Sun, 21 Jun 2020 17:54:01: 1000000 INFO @ Sun, 21 Jun 2020 17:54:07: 7000000 INFO @ Sun, 21 Jun 2020 17:54:07: 2000000 INFO @ Sun, 21 Jun 2020 17:54:14: 8000000 INFO @ Sun, 21 Jun 2020 17:54:14: 3000000 INFO @ Sun, 21 Jun 2020 17:54:20: 4000000 INFO @ Sun, 21 Jun 2020 17:54:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:54:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:54:20: #1 total tags in treatment: 8992917 INFO @ Sun, 21 Jun 2020 17:54:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:20: #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 17:54:21: #1 tags after filtering in treatment: 8992884 INFO @ Sun, 21 Jun 2020 17:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:22: #2 number of paired peaks: 4802 INFO @ Sun, 21 Jun 2020 17:54:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:22: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:22: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:22: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:22: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:54:22: #2 alternative fragment length(s) may be 3,11 bps INFO @ Sun, 21 Jun 2020 17:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.05_model.r WARNING @ Sun, 21 Jun 2020 17:54:22: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:54:22: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Sun, 21 Jun 2020 17:54:22: #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 17:54:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:22: #3 Pre-compute pvalue-qvalue table... 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 17:54:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.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 17:54:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:54:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:54:27: 5000000 INFO @ Sun, 21 Jun 2020 17:54:31: 1000000 INFO @ Sun, 21 Jun 2020 17:54:33: 6000000 INFO @ Sun, 21 Jun 2020 17:54:38: 2000000 INFO @ Sun, 21 Jun 2020 17:54:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:54:40: 7000000 INFO @ Sun, 21 Jun 2020 17:54:44: 3000000 INFO @ Sun, 21 Jun 2020 17:54:47: 8000000 INFO @ Sun, 21 Jun 2020 17:54:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:54:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:54:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.05_summits.bed INFO @ Sun, 21 Jun 2020 17:54:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:54:51: 4000000 INFO @ Sun, 21 Jun 2020 17:54:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:54:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:54:54: #1 total tags in treatment: 8992917 INFO @ Sun, 21 Jun 2020 17:54:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:54:54: #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 17:54:55: #1 tags after filtering in treatment: 8992884 INFO @ Sun, 21 Jun 2020 17:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:54:55: #1 finished! INFO @ Sun, 21 Jun 2020 17:54:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:54:56: #2 number of paired peaks: 4802 INFO @ Sun, 21 Jun 2020 17:54:56: start model_add_line... INFO @ Sun, 21 Jun 2020 17:54:56: start X-correlation... INFO @ Sun, 21 Jun 2020 17:54:56: end of X-cor INFO @ Sun, 21 Jun 2020 17:54:56: #2 finished! INFO @ Sun, 21 Jun 2020 17:54:56: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:54:56: #2 alternative fragment length(s) may be 3,11 bps INFO @ Sun, 21 Jun 2020 17:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.10_model.r WARNING @ Sun, 21 Jun 2020 17:54:56: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:54:56: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Sun, 21 Jun 2020 17:54:56: #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 17:54:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:54:57: 5000000 INFO @ Sun, 21 Jun 2020 17:55:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:55:09: 7000000 INFO @ Sun, 21 Jun 2020 17:55:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:15: 8000000 INFO @ Sun, 21 Jun 2020 17:55:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.10_summits.bed INFO @ Sun, 21 Jun 2020 17:55:21: Done! INFO @ Sun, 21 Jun 2020 17:55:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:55:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:55:22: #1 total tags in treatment: 8992917 INFO @ Sun, 21 Jun 2020 17:55:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:55:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:55:22: #1 tags after filtering in treatment: 8992884 INFO @ Sun, 21 Jun 2020 17:55:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:55:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:55:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:55:22: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:55:23: #2 number of paired peaks: 4802 INFO @ Sun, 21 Jun 2020 17:55:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:55:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:55:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:55:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:55:23: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:55:23: #2 alternative fragment length(s) may be 3,11 bps INFO @ Sun, 21 Jun 2020 17:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.20_model.r WARNING @ Sun, 21 Jun 2020 17:55:23: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:55:23: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Sun, 21 Jun 2020 17:55:23: #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 17:55:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:55:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX152097/SRX152097.20_summits.bed INFO @ Sun, 21 Jun 2020 17:55:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling