Job ID = 6529424 SRX = SRX2618507 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:35 44145239 reads; of these: 44145239 (100.00%) were unpaired; of these: 17488235 (39.62%) aligned 0 times 24228363 (54.88%) aligned exactly 1 time 2428641 (5.50%) aligned >1 times 60.38% overall alignment rate Time searching: 00:07:35 Overall time: 00:07:35 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 12 files... [bam_rmdupse_core] 3218831 / 26657004 = 0.1207 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, 30 Jun 2020 02:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.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, 30 Jun 2020 02:31:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:44: 1000000 INFO @ Tue, 30 Jun 2020 02:31:49: 2000000 INFO @ Tue, 30 Jun 2020 02:31:55: 3000000 INFO @ Tue, 30 Jun 2020 02:32:00: 4000000 INFO @ Tue, 30 Jun 2020 02:32:05: 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, 30 Jun 2020 02:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.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, 30 Jun 2020 02:32:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:11: 6000000 INFO @ Tue, 30 Jun 2020 02:32:15: 1000000 INFO @ Tue, 30 Jun 2020 02:32:17: 7000000 INFO @ Tue, 30 Jun 2020 02:32:20: 2000000 INFO @ Tue, 30 Jun 2020 02:32:23: 8000000 INFO @ Tue, 30 Jun 2020 02:32:26: 3000000 INFO @ Tue, 30 Jun 2020 02:32:29: 9000000 INFO @ Tue, 30 Jun 2020 02:32:32: 4000000 INFO @ Tue, 30 Jun 2020 02:32:34: 10000000 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, 30 Jun 2020 02:32:38: 5000000 INFO @ Tue, 30 Jun 2020 02:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.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, 30 Jun 2020 02:32:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:41: 11000000 INFO @ Tue, 30 Jun 2020 02:32:44: 6000000 INFO @ Tue, 30 Jun 2020 02:32:45: 1000000 INFO @ Tue, 30 Jun 2020 02:32:48: 12000000 INFO @ Tue, 30 Jun 2020 02:32:51: 7000000 INFO @ Tue, 30 Jun 2020 02:32:52: 2000000 INFO @ Tue, 30 Jun 2020 02:32:55: 13000000 INFO @ Tue, 30 Jun 2020 02:32:57: 8000000 INFO @ Tue, 30 Jun 2020 02:32:59: 3000000 INFO @ Tue, 30 Jun 2020 02:33:01: 14000000 INFO @ Tue, 30 Jun 2020 02:33:04: 9000000 INFO @ Tue, 30 Jun 2020 02:33:06: 4000000 INFO @ Tue, 30 Jun 2020 02:33:08: 15000000 INFO @ Tue, 30 Jun 2020 02:33:10: 10000000 INFO @ Tue, 30 Jun 2020 02:33:13: 5000000 INFO @ Tue, 30 Jun 2020 02:33:15: 16000000 INFO @ Tue, 30 Jun 2020 02:33:16: 11000000 INFO @ Tue, 30 Jun 2020 02:33:19: 6000000 INFO @ Tue, 30 Jun 2020 02:33:21: 17000000 INFO @ Tue, 30 Jun 2020 02:33:23: 12000000 INFO @ Tue, 30 Jun 2020 02:33:26: 7000000 INFO @ Tue, 30 Jun 2020 02:33:28: 18000000 INFO @ Tue, 30 Jun 2020 02:33:29: 13000000 INFO @ Tue, 30 Jun 2020 02:33:32: 8000000 INFO @ Tue, 30 Jun 2020 02:33:34: 19000000 INFO @ Tue, 30 Jun 2020 02:33:36: 14000000 INFO @ Tue, 30 Jun 2020 02:33:38: 9000000 INFO @ Tue, 30 Jun 2020 02:33:41: 20000000 INFO @ Tue, 30 Jun 2020 02:33:42: 15000000 INFO @ Tue, 30 Jun 2020 02:33:45: 10000000 INFO @ Tue, 30 Jun 2020 02:33:48: 21000000 INFO @ Tue, 30 Jun 2020 02:33:48: 16000000 INFO @ Tue, 30 Jun 2020 02:33:51: 11000000 INFO @ Tue, 30 Jun 2020 02:33:54: 22000000 INFO @ Tue, 30 Jun 2020 02:33:55: 17000000 INFO @ Tue, 30 Jun 2020 02:33:58: 12000000 INFO @ Tue, 30 Jun 2020 02:34:00: 23000000 INFO @ Tue, 30 Jun 2020 02:34:01: 18000000 INFO @ Tue, 30 Jun 2020 02:34:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:04: #1 total tags in treatment: 23438173 INFO @ Tue, 30 Jun 2020 02:34:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:04: 13000000 INFO @ Tue, 30 Jun 2020 02:34:05: #1 tags after filtering in treatment: 23438151 INFO @ Tue, 30 Jun 2020 02:34:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:06: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 02:34:06: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:06: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:07: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:34:07: #2 alternative fragment length(s) may be 2,59 bps INFO @ Tue, 30 Jun 2020 02:34:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.05_model.r WARNING @ Tue, 30 Jun 2020 02:34:07: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:07: #2 You may need to consider one of the other alternative d(s): 2,59 WARNING @ Tue, 30 Jun 2020 02:34:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:07: 19000000 INFO @ Tue, 30 Jun 2020 02:34:10: 14000000 INFO @ Tue, 30 Jun 2020 02:34:14: 20000000 INFO @ Tue, 30 Jun 2020 02:34:16: 15000000 INFO @ Tue, 30 Jun 2020 02:34:20: 21000000 INFO @ Tue, 30 Jun 2020 02:34:22: 16000000 INFO @ Tue, 30 Jun 2020 02:34:25: 22000000 INFO @ Tue, 30 Jun 2020 02:34:28: 17000000 INFO @ Tue, 30 Jun 2020 02:34:31: 23000000 INFO @ Tue, 30 Jun 2020 02:34:34: 18000000 INFO @ Tue, 30 Jun 2020 02:34:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:34: #1 total tags in treatment: 23438173 INFO @ Tue, 30 Jun 2020 02:34:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:34:35: #1 tags after filtering in treatment: 23438151 INFO @ Tue, 30 Jun 2020 02:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:35: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:37: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 02:34:37: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:37: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:34:37: #2 alternative fragment length(s) may be 2,59 bps INFO @ Tue, 30 Jun 2020 02:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.10_model.r WARNING @ Tue, 30 Jun 2020 02:34:37: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:37: #2 You may need to consider one of the other alternative d(s): 2,59 WARNING @ Tue, 30 Jun 2020 02:34:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:34:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:39: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:34:45: 20000000 INFO @ Tue, 30 Jun 2020 02:34:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:51: 21000000 INFO @ Tue, 30 Jun 2020 02:34:56: 22000000 INFO @ Tue, 30 Jun 2020 02:35:01: 23000000 INFO @ Tue, 30 Jun 2020 02:35:05: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:35:05: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:35:05: #1 total tags in treatment: 23438173 INFO @ Tue, 30 Jun 2020 02:35:05: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:35:05: #1 tags after filtering in treatment: 23438151 INFO @ Tue, 30 Jun 2020 02:35:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:07: #2 number of paired peaks: 135 WARNING @ Tue, 30 Jun 2020 02:35:07: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:07: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:35:07: #2 alternative fragment length(s) may be 2,59 bps INFO @ Tue, 30 Jun 2020 02:35:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.20_model.r WARNING @ Tue, 30 Jun 2020 02:35:07: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:35:07: #2 You may need to consider one of the other alternative d(s): 2,59 WARNING @ Tue, 30 Jun 2020 02:35:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:35:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.05_summits.bed INFO @ Tue, 30 Jun 2020 02:35:09: Done! pass1 - making usageList (239 chroms): 1 millis pass2 - checking and writing primary data (3330 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.10_summits.bed INFO @ Tue, 30 Jun 2020 02:35:38: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:36:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618507/SRX2618507.20_summits.bed INFO @ Tue, 30 Jun 2020 02:36:07: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 5 millis CompletedMACS2peakCalling