Job ID = 6454436 SRX = SRX2055964 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:08:09 prefetch.2.10.7: 1) Downloading 'SRR4069196'... 2020-06-21T09:08:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:17:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:17:06 prefetch.2.10.7: 1) 'SRR4069196' was downloaded successfully Read 24910232 spots for SRR4069196/SRR4069196.sra Written 24910232 spots for SRR4069196/SRR4069196.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: 00:00:01 Multiseed full-index search: 00:07:50 24910232 reads; of these: 24910232 (100.00%) were unpaired; of these: 1182720 (4.75%) aligned 0 times 14920478 (59.90%) aligned exactly 1 time 8807034 (35.36%) aligned >1 times 95.25% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 4621332 / 23727512 = 0.1948 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 18:31:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.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 18:31:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:32: 1000000 INFO @ Sun, 21 Jun 2020 18:31:38: 2000000 INFO @ Sun, 21 Jun 2020 18:31:43: 3000000 INFO @ Sun, 21 Jun 2020 18:31:48: 4000000 INFO @ Sun, 21 Jun 2020 18:31:53: 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 @ Sun, 21 Jun 2020 18:31:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.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 18:31:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:31:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:31:58: 6000000 INFO @ Sun, 21 Jun 2020 18:32:02: 1000000 INFO @ Sun, 21 Jun 2020 18:32:03: 7000000 INFO @ Sun, 21 Jun 2020 18:32:07: 2000000 INFO @ Sun, 21 Jun 2020 18:32:08: 8000000 INFO @ Sun, 21 Jun 2020 18:32:13: 3000000 INFO @ Sun, 21 Jun 2020 18:32:13: 9000000 INFO @ Sun, 21 Jun 2020 18:32:18: 4000000 INFO @ Sun, 21 Jun 2020 18:32:18: 10000000 INFO @ Sun, 21 Jun 2020 18:32:23: 5000000 INFO @ Sun, 21 Jun 2020 18:32:23: 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 @ Sun, 21 Jun 2020 18:32:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.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 18:32:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:32:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:32:28: 6000000 INFO @ Sun, 21 Jun 2020 18:32:28: 12000000 INFO @ Sun, 21 Jun 2020 18:32:32: 1000000 INFO @ Sun, 21 Jun 2020 18:32:33: 7000000 INFO @ Sun, 21 Jun 2020 18:32:33: 13000000 INFO @ Sun, 21 Jun 2020 18:32:37: 2000000 INFO @ Sun, 21 Jun 2020 18:32:38: 8000000 INFO @ Sun, 21 Jun 2020 18:32:38: 14000000 INFO @ Sun, 21 Jun 2020 18:32:42: 3000000 INFO @ Sun, 21 Jun 2020 18:32:43: 9000000 INFO @ Sun, 21 Jun 2020 18:32:43: 15000000 INFO @ Sun, 21 Jun 2020 18:32:47: 4000000 INFO @ Sun, 21 Jun 2020 18:32:48: 10000000 INFO @ Sun, 21 Jun 2020 18:32:49: 16000000 INFO @ Sun, 21 Jun 2020 18:32:53: 5000000 INFO @ Sun, 21 Jun 2020 18:32:53: 11000000 INFO @ Sun, 21 Jun 2020 18:32:54: 17000000 INFO @ Sun, 21 Jun 2020 18:32:58: 6000000 INFO @ Sun, 21 Jun 2020 18:32:58: 12000000 INFO @ Sun, 21 Jun 2020 18:32:59: 18000000 INFO @ Sun, 21 Jun 2020 18:33:03: 7000000 INFO @ Sun, 21 Jun 2020 18:33:03: 13000000 INFO @ Sun, 21 Jun 2020 18:33:04: 19000000 INFO @ Sun, 21 Jun 2020 18:33:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:05: #1 total tags in treatment: 19106180 INFO @ Sun, 21 Jun 2020 18:33:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:05: #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 18:33:06: #1 tags after filtering in treatment: 19106124 INFO @ Sun, 21 Jun 2020 18:33:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:07: #2 number of paired peaks: 1671 INFO @ Sun, 21 Jun 2020 18:33:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:07: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:33:07: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 18:33:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.05_model.r WARNING @ Sun, 21 Jun 2020 18:33:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:07: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 18:33:07: #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 18:33:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:08: 8000000 INFO @ Sun, 21 Jun 2020 18:33:08: 14000000 INFO @ Sun, 21 Jun 2020 18:33:13: 9000000 INFO @ Sun, 21 Jun 2020 18:33:13: 15000000 INFO @ Sun, 21 Jun 2020 18:33:18: 10000000 INFO @ Sun, 21 Jun 2020 18:33:19: 16000000 INFO @ Sun, 21 Jun 2020 18:33:23: 11000000 INFO @ Sun, 21 Jun 2020 18:33:24: 17000000 INFO @ Sun, 21 Jun 2020 18:33:28: 12000000 INFO @ Sun, 21 Jun 2020 18:33:29: 18000000 INFO @ Sun, 21 Jun 2020 18:33:33: 13000000 INFO @ Sun, 21 Jun 2020 18:33:34: 19000000 INFO @ Sun, 21 Jun 2020 18:33:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:33:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:33:35: #1 total tags in treatment: 19106180 INFO @ Sun, 21 Jun 2020 18:33:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:33:35: #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 18:33:36: #1 tags after filtering in treatment: 19106124 INFO @ Sun, 21 Jun 2020 18:33:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:33:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:33:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:33:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:33:37: #2 number of paired peaks: 1671 INFO @ Sun, 21 Jun 2020 18:33:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:33:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:33:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:33:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:33:37: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:33:37: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 18:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.10_model.r WARNING @ Sun, 21 Jun 2020 18:33:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:33:37: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 18:33:37: #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 18:33:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:33:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:33:38: 14000000 INFO @ Sun, 21 Jun 2020 18:33:43: 15000000 INFO @ Sun, 21 Jun 2020 18:33:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:33:48: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:33:53: 17000000 INFO @ Sun, 21 Jun 2020 18:33:58: 18000000 INFO @ Sun, 21 Jun 2020 18:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.05_summits.bed INFO @ Sun, 21 Jun 2020 18:34:02: Done! pass1 - making usageList (709 chroms): 2 millis pass2 - checking and writing primary data (3817 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:03: 19000000 INFO @ Sun, 21 Jun 2020 18:34:04: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:34:04: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:34:04: #1 total tags in treatment: 19106180 INFO @ Sun, 21 Jun 2020 18:34:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:34:04: #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 18:34:04: #1 tags after filtering in treatment: 19106124 INFO @ Sun, 21 Jun 2020 18:34:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:34:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:34:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:34:06: #2 number of paired peaks: 1671 INFO @ Sun, 21 Jun 2020 18:34:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:34:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:34:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:34:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:34:06: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:34:06: #2 alternative fragment length(s) may be 2,50 bps INFO @ Sun, 21 Jun 2020 18:34:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.20_model.r WARNING @ Sun, 21 Jun 2020 18:34:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:34:06: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Sun, 21 Jun 2020 18:34:06: #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 18:34:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:34:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:34:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:34:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:34:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:34:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.10_summits.bed INFO @ Sun, 21 Jun 2020 18:34:30: Done! BigWig に変換しました。 pass1 - making usageList (608 chroms): 1 millis pass2 - checking and writing primary data (2617 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:34:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2055964/SRX2055964.20_summits.bed INFO @ Sun, 21 Jun 2020 18:35:00: Done! pass1 - making usageList (457 chroms): 1 millis pass2 - checking and writing primary data (1590 records, 4 fields): 13 millis CompletedMACS2peakCalling