Job ID = 6454499 SRX = SRX2165283 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:18:09 prefetch.2.10.7: 1) Downloading 'SRR4244795'... 2020-06-21T09:18:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:04 prefetch.2.10.7: 'SRR4244795' is valid 2020-06-21T09:21:04 prefetch.2.10.7: 1) 'SRR4244795' was downloaded successfully Read 14169177 spots for SRR4244795/SRR4244795.sra Written 14169177 spots for SRR4244795/SRR4244795.sra 2020-06-21T09:22:00 prefetch.2.10.7: 1) Downloading 'SRR4244796'... 2020-06-21T09:22:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:26:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:26:42 prefetch.2.10.7: 1) 'SRR4244796' was downloaded successfully Read 24411219 spots for SRR4244796/SRR4244796.sra Written 24411219 spots for SRR4244796/SRR4244796.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: 00:14:32 38580396 reads; of these: 38580396 (100.00%) were unpaired; of these: 3086241 (8.00%) aligned 0 times 25988312 (67.36%) aligned exactly 1 time 9505843 (24.64%) aligned >1 times 92.00% overall alignment rate Time searching: 00:14:32 Overall time: 00:14:32 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 16 files... [bam_rmdupse_core] 23213055 / 35494155 = 0.6540 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 18:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.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 18:50:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:50:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:50:37: 1000000 INFO @ Sun, 21 Jun 2020 18:50:43: 2000000 INFO @ Sun, 21 Jun 2020 18:50:50: 3000000 INFO @ Sun, 21 Jun 2020 18:50:57: 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 @ Sun, 21 Jun 2020 18:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.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 18:51:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:03: 5000000 INFO @ Sun, 21 Jun 2020 18:51:07: 1000000 INFO @ Sun, 21 Jun 2020 18:51:10: 6000000 INFO @ Sun, 21 Jun 2020 18:51:14: 2000000 INFO @ Sun, 21 Jun 2020 18:51:17: 7000000 INFO @ Sun, 21 Jun 2020 18:51:22: 3000000 INFO @ Sun, 21 Jun 2020 18:51:24: 8000000 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 18:51:28: 4000000 INFO @ Sun, 21 Jun 2020 18:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.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 18:51:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:51:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:51:30: 9000000 INFO @ Sun, 21 Jun 2020 18:51:35: 5000000 INFO @ Sun, 21 Jun 2020 18:51:38: 1000000 INFO @ Sun, 21 Jun 2020 18:51:38: 10000000 INFO @ Sun, 21 Jun 2020 18:51:43: 6000000 INFO @ Sun, 21 Jun 2020 18:51:45: 11000000 INFO @ Sun, 21 Jun 2020 18:51:46: 2000000 INFO @ Sun, 21 Jun 2020 18:51:50: 7000000 INFO @ Sun, 21 Jun 2020 18:51:52: 12000000 INFO @ Sun, 21 Jun 2020 18:51:53: 3000000 INFO @ Sun, 21 Jun 2020 18:51:55: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:51:55: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:51:55: #1 total tags in treatment: 12281100 INFO @ Sun, 21 Jun 2020 18:51:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:51:55: #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 18:51:55: #1 tags after filtering in treatment: 12281100 INFO @ Sun, 21 Jun 2020 18:51:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:51:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:51:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:51:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:51:56: #2 number of paired peaks: 1191 INFO @ Sun, 21 Jun 2020 18:51:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:51:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:51:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:51:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:51:56: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:51:56: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 18:51:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.05_model.r WARNING @ Sun, 21 Jun 2020 18:51:56: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:51:56: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 18:51:56: #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 18:51:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:51:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:51:57: 8000000 INFO @ Sun, 21 Jun 2020 18:52:00: 4000000 INFO @ Sun, 21 Jun 2020 18:52:04: 9000000 INFO @ Sun, 21 Jun 2020 18:52:07: 5000000 INFO @ Sun, 21 Jun 2020 18:52:11: 10000000 INFO @ Sun, 21 Jun 2020 18:52:14: 6000000 INFO @ Sun, 21 Jun 2020 18:52:18: 11000000 INFO @ Sun, 21 Jun 2020 18:52:21: 7000000 INFO @ Sun, 21 Jun 2020 18:52:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:25: 12000000 INFO @ Sun, 21 Jun 2020 18:52:27: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:52:27: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:52:27: #1 total tags in treatment: 12281100 INFO @ Sun, 21 Jun 2020 18:52:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:27: #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 18:52:27: #1 tags after filtering in treatment: 12281100 INFO @ Sun, 21 Jun 2020 18:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:27: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:28: 8000000 INFO @ Sun, 21 Jun 2020 18:52:28: #2 number of paired peaks: 1191 INFO @ Sun, 21 Jun 2020 18:52:28: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:29: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:52:29: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 18:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.10_model.r WARNING @ Sun, 21 Jun 2020 18:52:29: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:29: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 18:52:29: #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 18:52:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:52:34: 9000000 INFO @ Sun, 21 Jun 2020 18:52:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:52:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:52:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.05_summits.bed INFO @ Sun, 21 Jun 2020 18:52:39: Done! pass1 - making usageList (863 chroms): 1 millis pass2 - checking and writing primary data (3303 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:52:41: 10000000 INFO @ Sun, 21 Jun 2020 18:52:47: 11000000 INFO @ Sun, 21 Jun 2020 18:52:54: 12000000 INFO @ Sun, 21 Jun 2020 18:52:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:52:56: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 18:52:56: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 18:52:56: #1 total tags in treatment: 12281100 INFO @ Sun, 21 Jun 2020 18:52:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:52:56: #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 18:52:56: #1 tags after filtering in treatment: 12281100 INFO @ Sun, 21 Jun 2020 18:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:52:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:52:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:52:57: #2 number of paired peaks: 1191 INFO @ Sun, 21 Jun 2020 18:52:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:52:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:52:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:52:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:52:57: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 18:52:57: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 18:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.20_model.r WARNING @ Sun, 21 Jun 2020 18:52:57: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:52:57: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 18:52:57: #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 18:52:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.10_summits.bed INFO @ Sun, 21 Jun 2020 18:53:08: Done! BigWig に変換しました。 pass1 - making usageList (680 chroms): 1 millis pass2 - checking and writing primary data (2142 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:53:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165283/SRX2165283.20_summits.bed INFO @ Sun, 21 Jun 2020 18:53:36: Done! pass1 - making usageList (554 chroms): 2 millis pass2 - checking and writing primary data (1481 records, 4 fields): 17 millis CompletedMACS2peakCalling