Job ID = 6498698 SRX = SRX706810 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:53:44 prefetch.2.10.7: 1) Downloading 'SRR1581491'... 2020-06-25T23:53:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:52 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:52 prefetch.2.10.7: 1) 'SRR1581491' was downloaded successfully Read 23681642 spots for SRR1581491/SRR1581491.sra Written 23681642 spots for SRR1581491/SRR1581491.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: 00:05:43 23681642 reads; of these: 23681642 (100.00%) were unpaired; of these: 7521716 (31.76%) aligned 0 times 11045358 (46.64%) aligned exactly 1 time 5114568 (21.60%) aligned >1 times 68.24% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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 8 files... [bam_rmdupse_core] 7860232 / 16159926 = 0.4864 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 09:06:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.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 09:06:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:18: 1000000 INFO @ Fri, 26 Jun 2020 09:06:23: 2000000 INFO @ Fri, 26 Jun 2020 09:06:28: 3000000 INFO @ Fri, 26 Jun 2020 09:06:33: 4000000 INFO @ Fri, 26 Jun 2020 09:06:38: 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 @ Fri, 26 Jun 2020 09:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.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 09:06:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:06:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:06:43: 6000000 INFO @ Fri, 26 Jun 2020 09:06:49: 1000000 INFO @ Fri, 26 Jun 2020 09:06:49: 7000000 INFO @ Fri, 26 Jun 2020 09:06:54: 8000000 INFO @ Fri, 26 Jun 2020 09:06:54: 2000000 INFO @ Fri, 26 Jun 2020 09:06:56: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:06:56: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:06:56: #1 total tags in treatment: 8299694 INFO @ Fri, 26 Jun 2020 09:06:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:06:56: #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 09:06:56: #1 tags after filtering in treatment: 8299694 INFO @ Fri, 26 Jun 2020 09:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:06:56: #1 finished! INFO @ Fri, 26 Jun 2020 09:06:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:06:56: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 09:06:56: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 09:06:56: start model_add_line... INFO @ Fri, 26 Jun 2020 09:06:56: start X-correlation... INFO @ Fri, 26 Jun 2020 09:06:57: end of X-cor INFO @ Fri, 26 Jun 2020 09:06:57: #2 finished! INFO @ Fri, 26 Jun 2020 09:06:57: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 09:06:57: #2 alternative fragment length(s) may be 3,54 bps INFO @ Fri, 26 Jun 2020 09:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.05_model.r WARNING @ Fri, 26 Jun 2020 09:06:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:06:57: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Fri, 26 Jun 2020 09:06:57: #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 09:06:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:07:00: 3000000 INFO @ Fri, 26 Jun 2020 09:07:05: 4000000 INFO @ Fri, 26 Jun 2020 09:07:10: 5000000 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 09:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.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 09:07:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:07:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:07:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:07:15: 6000000 INFO @ Fri, 26 Jun 2020 09:07:19: 1000000 INFO @ Fri, 26 Jun 2020 09:07:20: 7000000 INFO @ Fri, 26 Jun 2020 09:07:24: 2000000 INFO @ Fri, 26 Jun 2020 09:07:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:07:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:07:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.05_summits.bed INFO @ Fri, 26 Jun 2020 09:07:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2212 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:07:26: 8000000 INFO @ Fri, 26 Jun 2020 09:07:27: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:07:27: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:07:27: #1 total tags in treatment: 8299694 INFO @ Fri, 26 Jun 2020 09:07:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:07:27: #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 09:07:27: #1 tags after filtering in treatment: 8299694 INFO @ Fri, 26 Jun 2020 09:07:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:07:27: #1 finished! INFO @ Fri, 26 Jun 2020 09:07:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:07:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:07:28: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 09:07:28: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 09:07:28: start model_add_line... INFO @ Fri, 26 Jun 2020 09:07:28: start X-correlation... INFO @ Fri, 26 Jun 2020 09:07:28: end of X-cor INFO @ Fri, 26 Jun 2020 09:07:28: #2 finished! INFO @ Fri, 26 Jun 2020 09:07:28: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 09:07:28: #2 alternative fragment length(s) may be 3,54 bps INFO @ Fri, 26 Jun 2020 09:07:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.10_model.r WARNING @ Fri, 26 Jun 2020 09:07:28: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:07:28: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Fri, 26 Jun 2020 09:07:28: #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 09:07:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:07:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:07:29: 3000000 INFO @ Fri, 26 Jun 2020 09:07:34: 4000000 INFO @ Fri, 26 Jun 2020 09:07:39: 5000000 INFO @ Fri, 26 Jun 2020 09:07:45: 6000000 INFO @ Fri, 26 Jun 2020 09:07:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:07:50: 7000000 INFO @ Fri, 26 Jun 2020 09:07:55: 8000000 INFO @ Fri, 26 Jun 2020 09:07:57: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:07:57: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:07:57: #1 total tags in treatment: 8299694 INFO @ Fri, 26 Jun 2020 09:07:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:07:57: #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 09:07:57: #1 tags after filtering in treatment: 8299694 INFO @ Fri, 26 Jun 2020 09:07:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:07:57: #1 finished! INFO @ Fri, 26 Jun 2020 09:07:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:07:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:07:57: #2 number of paired peaks: 328 WARNING @ Fri, 26 Jun 2020 09:07:57: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Fri, 26 Jun 2020 09:07:57: start model_add_line... INFO @ Fri, 26 Jun 2020 09:07:58: start X-correlation... INFO @ Fri, 26 Jun 2020 09:07:58: end of X-cor INFO @ Fri, 26 Jun 2020 09:07:58: #2 finished! INFO @ Fri, 26 Jun 2020 09:07:58: #2 predicted fragment length is 54 bps INFO @ Fri, 26 Jun 2020 09:07:58: #2 alternative fragment length(s) may be 3,54 bps INFO @ Fri, 26 Jun 2020 09:07:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.20_model.r WARNING @ Fri, 26 Jun 2020 09:07:58: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:07:58: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Fri, 26 Jun 2020 09:07:58: #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 09:07:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:07:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.10_summits.bed INFO @ Fri, 26 Jun 2020 09:07:58: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (443 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:08:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706810/SRX706810.20_summits.bed INFO @ Fri, 26 Jun 2020 09:08:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 1 millis CompletedMACS2peakCalling