Job ID = 6529713 SRX = SRX4047178 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: 00:35:36 96672516 reads; of these: 96672516 (100.00%) were unpaired; of these: 16854540 (17.43%) aligned 0 times 49275000 (50.97%) aligned exactly 1 time 30542976 (31.59%) aligned >1 times 82.57% overall alignment rate Time searching: 00:35:36 Overall time: 00:35:36 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 36 files... [bam_rmdupse_core] 55661009 / 79817976 = 0.6973 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 03:28:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.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 03:28:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:29: 1000000 INFO @ Tue, 30 Jun 2020 03:28:35: 2000000 INFO @ Tue, 30 Jun 2020 03:28:41: 3000000 INFO @ Tue, 30 Jun 2020 03:28:46: 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 @ Tue, 30 Jun 2020 03:28:52: 5000000 INFO @ Tue, 30 Jun 2020 03:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.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 03:28:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:58: 6000000 INFO @ Tue, 30 Jun 2020 03:29:00: 1000000 INFO @ Tue, 30 Jun 2020 03:29:05: 7000000 INFO @ Tue, 30 Jun 2020 03:29:06: 2000000 INFO @ Tue, 30 Jun 2020 03:29:11: 8000000 INFO @ Tue, 30 Jun 2020 03:29:12: 3000000 INFO @ Tue, 30 Jun 2020 03:29:17: 9000000 INFO @ Tue, 30 Jun 2020 03:29:19: 4000000 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 03:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.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 03:29:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:29:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:29:23: 10000000 INFO @ Tue, 30 Jun 2020 03:29:25: 5000000 INFO @ Tue, 30 Jun 2020 03:29:30: 11000000 INFO @ Tue, 30 Jun 2020 03:29:30: 1000000 INFO @ Tue, 30 Jun 2020 03:29:31: 6000000 INFO @ Tue, 30 Jun 2020 03:29:36: 12000000 INFO @ Tue, 30 Jun 2020 03:29:36: 2000000 INFO @ Tue, 30 Jun 2020 03:29:38: 7000000 INFO @ Tue, 30 Jun 2020 03:29:42: 13000000 INFO @ Tue, 30 Jun 2020 03:29:43: 3000000 INFO @ Tue, 30 Jun 2020 03:29:44: 8000000 INFO @ Tue, 30 Jun 2020 03:29:49: 14000000 INFO @ Tue, 30 Jun 2020 03:29:49: 4000000 INFO @ Tue, 30 Jun 2020 03:29:51: 9000000 INFO @ Tue, 30 Jun 2020 03:29:55: 15000000 INFO @ Tue, 30 Jun 2020 03:29:56: 5000000 INFO @ Tue, 30 Jun 2020 03:29:57: 10000000 INFO @ Tue, 30 Jun 2020 03:30:02: 16000000 INFO @ Tue, 30 Jun 2020 03:30:02: 6000000 INFO @ Tue, 30 Jun 2020 03:30:03: 11000000 INFO @ Tue, 30 Jun 2020 03:30:08: 17000000 INFO @ Tue, 30 Jun 2020 03:30:08: 7000000 INFO @ Tue, 30 Jun 2020 03:30:10: 12000000 INFO @ Tue, 30 Jun 2020 03:30:14: 18000000 INFO @ Tue, 30 Jun 2020 03:30:15: 8000000 INFO @ Tue, 30 Jun 2020 03:30:16: 13000000 INFO @ Tue, 30 Jun 2020 03:30:21: 19000000 INFO @ Tue, 30 Jun 2020 03:30:21: 9000000 INFO @ Tue, 30 Jun 2020 03:30:23: 14000000 INFO @ Tue, 30 Jun 2020 03:30:28: 10000000 INFO @ Tue, 30 Jun 2020 03:30:28: 20000000 INFO @ Tue, 30 Jun 2020 03:30:29: 15000000 INFO @ Tue, 30 Jun 2020 03:30:34: 11000000 INFO @ Tue, 30 Jun 2020 03:30:34: 21000000 INFO @ Tue, 30 Jun 2020 03:30:36: 16000000 INFO @ Tue, 30 Jun 2020 03:30:41: 12000000 INFO @ Tue, 30 Jun 2020 03:30:41: 22000000 INFO @ Tue, 30 Jun 2020 03:30:42: 17000000 INFO @ Tue, 30 Jun 2020 03:30:47: 13000000 INFO @ Tue, 30 Jun 2020 03:30:47: 23000000 INFO @ Tue, 30 Jun 2020 03:30:49: 18000000 INFO @ Tue, 30 Jun 2020 03:30:53: 14000000 INFO @ Tue, 30 Jun 2020 03:30:54: 24000000 INFO @ Tue, 30 Jun 2020 03:30:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:30:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:30:55: #1 total tags in treatment: 24156967 INFO @ Tue, 30 Jun 2020 03:30:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:30:55: #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 03:30:56: 19000000 INFO @ Tue, 30 Jun 2020 03:30:56: #1 tags after filtering in treatment: 24156966 INFO @ Tue, 30 Jun 2020 03:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:30:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:30:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:30:58: #2 number of paired peaks: 1302 INFO @ Tue, 30 Jun 2020 03:30:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:30:58: start X-correlation... INFO @ Tue, 30 Jun 2020 03:30:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:30:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:30:58: #2 predicted fragment length is 74 bps INFO @ Tue, 30 Jun 2020 03:30:58: #2 alternative fragment length(s) may be 2,74 bps INFO @ Tue, 30 Jun 2020 03:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.05_model.r WARNING @ Tue, 30 Jun 2020 03:30:58: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:30:58: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Tue, 30 Jun 2020 03:30:58: #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 03:30:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:31:00: 15000000 INFO @ Tue, 30 Jun 2020 03:31:02: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:31:06: 16000000 INFO @ Tue, 30 Jun 2020 03:31:09: 21000000 INFO @ Tue, 30 Jun 2020 03:31:12: 17000000 INFO @ Tue, 30 Jun 2020 03:31:15: 22000000 INFO @ Tue, 30 Jun 2020 03:31:18: 18000000 INFO @ Tue, 30 Jun 2020 03:31:21: 23000000 INFO @ Tue, 30 Jun 2020 03:31:25: 19000000 INFO @ Tue, 30 Jun 2020 03:31:28: 24000000 INFO @ Tue, 30 Jun 2020 03:31:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:31:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:31:29: #1 total tags in treatment: 24156967 INFO @ Tue, 30 Jun 2020 03:31:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:31:29: #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 03:31:30: #1 tags after filtering in treatment: 24156966 INFO @ Tue, 30 Jun 2020 03:31:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:31:30: #1 finished! INFO @ Tue, 30 Jun 2020 03:31:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:31:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:31:31: 20000000 INFO @ Tue, 30 Jun 2020 03:31:31: #2 number of paired peaks: 1302 INFO @ Tue, 30 Jun 2020 03:31:31: start model_add_line... INFO @ Tue, 30 Jun 2020 03:31:31: start X-correlation... INFO @ Tue, 30 Jun 2020 03:31:31: end of X-cor INFO @ Tue, 30 Jun 2020 03:31:31: #2 finished! INFO @ Tue, 30 Jun 2020 03:31:31: #2 predicted fragment length is 74 bps INFO @ Tue, 30 Jun 2020 03:31:31: #2 alternative fragment length(s) may be 2,74 bps INFO @ Tue, 30 Jun 2020 03:31:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.10_model.r WARNING @ Tue, 30 Jun 2020 03:31:31: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:31:31: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Tue, 30 Jun 2020 03:31:31: #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 03:31:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:31:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:31:37: 21000000 INFO @ Tue, 30 Jun 2020 03:31:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:31:42: 22000000 INFO @ Tue, 30 Jun 2020 03:31:48: 23000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:31:54: 24000000 INFO @ Tue, 30 Jun 2020 03:31:55: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:31:55: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:31:55: #1 total tags in treatment: 24156967 INFO @ Tue, 30 Jun 2020 03:31:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:31:55: #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 03:31:56: #1 tags after filtering in treatment: 24156966 INFO @ Tue, 30 Jun 2020 03:31:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:31:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:31:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:31:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:31:57: #2 number of paired peaks: 1302 INFO @ Tue, 30 Jun 2020 03:31:57: start model_add_line... INFO @ Tue, 30 Jun 2020 03:31:57: start X-correlation... INFO @ Tue, 30 Jun 2020 03:31:58: end of X-cor INFO @ Tue, 30 Jun 2020 03:31:58: #2 finished! INFO @ Tue, 30 Jun 2020 03:31:58: #2 predicted fragment length is 74 bps INFO @ Tue, 30 Jun 2020 03:31:58: #2 alternative fragment length(s) may be 2,74 bps INFO @ Tue, 30 Jun 2020 03:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.20_model.r WARNING @ Tue, 30 Jun 2020 03:31:58: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:31:58: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Tue, 30 Jun 2020 03:31:58: #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 03:31:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:32:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.05_summits.bed INFO @ Tue, 30 Jun 2020 03:32:02: Done! pass1 - making usageList (1023 chroms): 2 millis pass2 - checking and writing primary data (11573 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:32:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.10_summits.bed INFO @ Tue, 30 Jun 2020 03:32:35: Done! pass1 - making usageList (883 chroms): 1 millis pass2 - checking and writing primary data (4019 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:32:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:33:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:33:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:33:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4047178/SRX4047178.20_summits.bed INFO @ Tue, 30 Jun 2020 03:33:02: Done! pass1 - making usageList (747 chroms): 2 millis pass2 - checking and writing primary data (2159 records, 4 fields): 21 millis CompletedMACS2peakCalling