Job ID = 6626456 SRX = SRX1532034 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22251827 spots for SRR3103384/SRR3103384.sra Written 22251827 spots for SRR3103384/SRR3103384.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626613 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:16 22251827 reads; of these: 22251827 (100.00%) were unpaired; of these: 854464 (3.84%) aligned 0 times 14358253 (64.53%) aligned exactly 1 time 7039110 (31.63%) aligned >1 times 96.16% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 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] 2115196 / 21397363 = 0.0989 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 @ Tue, 14 Jul 2020 07:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.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 @ Tue, 14 Jul 2020 07:16:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:16:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:02: 1000000 INFO @ Tue, 14 Jul 2020 07:17:07: 2000000 INFO @ Tue, 14 Jul 2020 07:17:12: 3000000 INFO @ Tue, 14 Jul 2020 07:17:17: 4000000 INFO @ Tue, 14 Jul 2020 07:17:22: 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 @ Tue, 14 Jul 2020 07:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.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 @ Tue, 14 Jul 2020 07:17:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:27: 6000000 INFO @ Tue, 14 Jul 2020 07:17:32: 1000000 INFO @ Tue, 14 Jul 2020 07:17:32: 7000000 INFO @ Tue, 14 Jul 2020 07:17:37: 2000000 INFO @ Tue, 14 Jul 2020 07:17:37: 8000000 INFO @ Tue, 14 Jul 2020 07:17:42: 3000000 INFO @ Tue, 14 Jul 2020 07:17:42: 9000000 INFO @ Tue, 14 Jul 2020 07:17:47: 4000000 INFO @ Tue, 14 Jul 2020 07:17:48: 10000000 INFO @ Tue, 14 Jul 2020 07:17:52: 5000000 INFO @ Tue, 14 Jul 2020 07:17:53: 11000000 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 @ Tue, 14 Jul 2020 07:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.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 @ Tue, 14 Jul 2020 07:17:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:17:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:17:57: 6000000 INFO @ Tue, 14 Jul 2020 07:17:58: 12000000 INFO @ Tue, 14 Jul 2020 07:18:02: 1000000 INFO @ Tue, 14 Jul 2020 07:18:02: 7000000 INFO @ Tue, 14 Jul 2020 07:18:03: 13000000 INFO @ Tue, 14 Jul 2020 07:18:07: 2000000 INFO @ Tue, 14 Jul 2020 07:18:08: 8000000 INFO @ Tue, 14 Jul 2020 07:18:08: 14000000 INFO @ Tue, 14 Jul 2020 07:18:12: 3000000 INFO @ Tue, 14 Jul 2020 07:18:13: 9000000 INFO @ Tue, 14 Jul 2020 07:18:14: 15000000 INFO @ Tue, 14 Jul 2020 07:18:17: 4000000 INFO @ Tue, 14 Jul 2020 07:18:18: 10000000 INFO @ Tue, 14 Jul 2020 07:18:19: 16000000 INFO @ Tue, 14 Jul 2020 07:18:22: 5000000 INFO @ Tue, 14 Jul 2020 07:18:23: 11000000 INFO @ Tue, 14 Jul 2020 07:18:24: 17000000 INFO @ Tue, 14 Jul 2020 07:18:28: 6000000 INFO @ Tue, 14 Jul 2020 07:18:28: 12000000 INFO @ Tue, 14 Jul 2020 07:18:29: 18000000 INFO @ Tue, 14 Jul 2020 07:18:33: 7000000 INFO @ Tue, 14 Jul 2020 07:18:33: 13000000 INFO @ Tue, 14 Jul 2020 07:18:35: 19000000 INFO @ Tue, 14 Jul 2020 07:18:36: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:18:36: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:18:36: #1 total tags in treatment: 19282167 INFO @ Tue, 14 Jul 2020 07:18:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:18:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:18:37: #1 tags after filtering in treatment: 19282167 INFO @ Tue, 14 Jul 2020 07:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:18:37: #1 finished! INFO @ Tue, 14 Jul 2020 07:18:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:18:38: 8000000 INFO @ Tue, 14 Jul 2020 07:18:38: #2 number of paired peaks: 665 WARNING @ Tue, 14 Jul 2020 07:18:38: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 14 Jul 2020 07:18:38: start model_add_line... INFO @ Tue, 14 Jul 2020 07:18:38: start X-correlation... INFO @ Tue, 14 Jul 2020 07:18:38: end of X-cor INFO @ Tue, 14 Jul 2020 07:18:38: #2 finished! INFO @ Tue, 14 Jul 2020 07:18:38: #2 predicted fragment length is 43 bps INFO @ Tue, 14 Jul 2020 07:18:38: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 14 Jul 2020 07:18:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.05_model.r WARNING @ Tue, 14 Jul 2020 07:18:38: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:18:38: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 14 Jul 2020 07:18:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:18:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:18:39: 14000000 INFO @ Tue, 14 Jul 2020 07:18:43: 9000000 INFO @ Tue, 14 Jul 2020 07:18:44: 15000000 INFO @ Tue, 14 Jul 2020 07:18:48: 10000000 INFO @ Tue, 14 Jul 2020 07:18:49: 16000000 INFO @ Tue, 14 Jul 2020 07:18:53: 11000000 INFO @ Tue, 14 Jul 2020 07:18:54: 17000000 INFO @ Tue, 14 Jul 2020 07:18:58: 12000000 INFO @ Tue, 14 Jul 2020 07:18:59: 18000000 INFO @ Tue, 14 Jul 2020 07:19:03: 13000000 INFO @ Tue, 14 Jul 2020 07:19:05: 19000000 INFO @ Tue, 14 Jul 2020 07:19:06: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:19:06: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:19:06: #1 total tags in treatment: 19282167 INFO @ Tue, 14 Jul 2020 07:19:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:19:07: #1 tags after filtering in treatment: 19282167 INFO @ Tue, 14 Jul 2020 07:19:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:19:07: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:08: #2 number of paired peaks: 665 WARNING @ Tue, 14 Jul 2020 07:19:08: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 14 Jul 2020 07:19:08: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:08: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:08: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:08: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:08: #2 predicted fragment length is 43 bps INFO @ Tue, 14 Jul 2020 07:19:08: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 14 Jul 2020 07:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.10_model.r WARNING @ Tue, 14 Jul 2020 07:19:08: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:19:08: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 14 Jul 2020 07:19:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:19:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:19:09: 14000000 INFO @ Tue, 14 Jul 2020 07:19:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:19:13: 15000000 INFO @ Tue, 14 Jul 2020 07:19:18: 16000000 INFO @ Tue, 14 Jul 2020 07:19:23: 17000000 INFO @ Tue, 14 Jul 2020 07:19:28: 18000000 INFO @ Tue, 14 Jul 2020 07:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.05_summits.bed INFO @ Tue, 14 Jul 2020 07:19:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3887 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:19:33: 19000000 INFO @ Tue, 14 Jul 2020 07:19:35: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:19:35: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:19:35: #1 total tags in treatment: 19282167 INFO @ Tue, 14 Jul 2020 07:19:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:19:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:19:35: #1 tags after filtering in treatment: 19282167 INFO @ Tue, 14 Jul 2020 07:19:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:19:35: #1 finished! INFO @ Tue, 14 Jul 2020 07:19:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:19:37: #2 number of paired peaks: 665 WARNING @ Tue, 14 Jul 2020 07:19:37: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Tue, 14 Jul 2020 07:19:37: start model_add_line... INFO @ Tue, 14 Jul 2020 07:19:37: start X-correlation... INFO @ Tue, 14 Jul 2020 07:19:37: end of X-cor INFO @ Tue, 14 Jul 2020 07:19:37: #2 finished! INFO @ Tue, 14 Jul 2020 07:19:37: #2 predicted fragment length is 43 bps INFO @ Tue, 14 Jul 2020 07:19:37: #2 alternative fragment length(s) may be 2,43 bps INFO @ Tue, 14 Jul 2020 07:19:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.20_model.r WARNING @ Tue, 14 Jul 2020 07:19:37: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:19:37: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Tue, 14 Jul 2020 07:19:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:19:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:19:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:19:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:20:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.10_summits.bed INFO @ Tue, 14 Jul 2020 07:20:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2217 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:20:11: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:20:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:20:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:20:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1532034/SRX1532034.20_summits.bed INFO @ Tue, 14 Jul 2020 07:20:28: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (753 records, 4 fields): 21 millis CompletedMACS2peakCalling