Job ID = 6457020 SRX = SRX4315043 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:40:28 prefetch.2.10.7: 1) Downloading 'SRR7444504'... 2020-06-21T11:40:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:43:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:43:55 prefetch.2.10.7: 1) 'SRR7444504' was downloaded successfully 2020-06-21T11:44:32 prefetch.2.10.7: 'SRR7444504' has 7 unresolved dependencies 2020-06-21T11:44:32 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:44:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:44:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:44:49 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:44:49 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:44:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:07 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:45:07 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:45:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:20 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:45:20 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:45:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:38 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:45:38 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:45:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:45:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:45:57 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:45:57 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:45:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:46:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:46:17 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:46:17 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:46:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:46:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:46:31 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 40096891 spots for SRR7444504/SRR7444504.sra Written 40096891 spots for SRR7444504/SRR7444504.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: 00:08:06 40096891 reads; of these: 40096891 (100.00%) were unpaired; of these: 8255 (0.02%) aligned 0 times 36772810 (91.71%) aligned exactly 1 time 3315826 (8.27%) aligned >1 times 99.98% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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 20 files... [bam_rmdupse_core] 19592871 / 40088636 = 0.4887 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 21:05:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.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 21:05:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:05:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:05:55: 1000000 INFO @ Sun, 21 Jun 2020 21:06:01: 2000000 INFO @ Sun, 21 Jun 2020 21:06:07: 3000000 INFO @ Sun, 21 Jun 2020 21:06:13: 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 21:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.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 21:06:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:19: 5000000 INFO @ Sun, 21 Jun 2020 21:06:27: 6000000 INFO @ Sun, 21 Jun 2020 21:06:27: 1000000 INFO @ Sun, 21 Jun 2020 21:06:34: 7000000 INFO @ Sun, 21 Jun 2020 21:06:35: 2000000 INFO @ Sun, 21 Jun 2020 21:06:42: 8000000 INFO @ Sun, 21 Jun 2020 21:06:43: 3000000 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 21:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.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 21:06:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:06:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:06:49: 9000000 INFO @ Sun, 21 Jun 2020 21:06:52: 4000000 INFO @ Sun, 21 Jun 2020 21:06:57: 10000000 INFO @ Sun, 21 Jun 2020 21:06:57: 1000000 INFO @ Sun, 21 Jun 2020 21:07:00: 5000000 INFO @ Sun, 21 Jun 2020 21:07:04: 11000000 INFO @ Sun, 21 Jun 2020 21:07:05: 2000000 INFO @ Sun, 21 Jun 2020 21:07:09: 6000000 INFO @ Sun, 21 Jun 2020 21:07:12: 12000000 INFO @ Sun, 21 Jun 2020 21:07:14: 3000000 INFO @ Sun, 21 Jun 2020 21:07:17: 7000000 INFO @ Sun, 21 Jun 2020 21:07:20: 13000000 INFO @ Sun, 21 Jun 2020 21:07:22: 4000000 INFO @ Sun, 21 Jun 2020 21:07:25: 8000000 INFO @ Sun, 21 Jun 2020 21:07:27: 14000000 INFO @ Sun, 21 Jun 2020 21:07:31: 5000000 INFO @ Sun, 21 Jun 2020 21:07:34: 9000000 INFO @ Sun, 21 Jun 2020 21:07:35: 15000000 INFO @ Sun, 21 Jun 2020 21:07:39: 6000000 INFO @ Sun, 21 Jun 2020 21:07:42: 16000000 INFO @ Sun, 21 Jun 2020 21:07:43: 10000000 INFO @ Sun, 21 Jun 2020 21:07:48: 7000000 INFO @ Sun, 21 Jun 2020 21:07:50: 17000000 INFO @ Sun, 21 Jun 2020 21:07:51: 11000000 INFO @ Sun, 21 Jun 2020 21:07:56: 8000000 INFO @ Sun, 21 Jun 2020 21:07:58: 18000000 INFO @ Sun, 21 Jun 2020 21:07:59: 12000000 INFO @ Sun, 21 Jun 2020 21:08:05: 9000000 INFO @ Sun, 21 Jun 2020 21:08:05: 19000000 INFO @ Sun, 21 Jun 2020 21:08:08: 13000000 INFO @ Sun, 21 Jun 2020 21:08:13: 20000000 INFO @ Sun, 21 Jun 2020 21:08:13: 10000000 INFO @ Sun, 21 Jun 2020 21:08:16: 14000000 INFO @ Sun, 21 Jun 2020 21:08:17: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:08:17: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:08:17: #1 total tags in treatment: 20495765 INFO @ Sun, 21 Jun 2020 21:08:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:17: #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 21:08:17: #1 tags after filtering in treatment: 20495601 INFO @ Sun, 21 Jun 2020 21:08:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:17: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:19: #2 number of paired peaks: 5732 INFO @ Sun, 21 Jun 2020 21:08:19: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:19: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:19: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:19: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:19: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:08:19: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.05_model.r WARNING @ Sun, 21 Jun 2020 21:08:19: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:08:19: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Sun, 21 Jun 2020 21:08:19: #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 21:08:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:21: 11000000 INFO @ Sun, 21 Jun 2020 21:08:24: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:08:29: 12000000 INFO @ Sun, 21 Jun 2020 21:08:32: 16000000 INFO @ Sun, 21 Jun 2020 21:08:37: 13000000 INFO @ Sun, 21 Jun 2020 21:08:40: 17000000 INFO @ Sun, 21 Jun 2020 21:08:45: 14000000 INFO @ Sun, 21 Jun 2020 21:08:48: 18000000 INFO @ Sun, 21 Jun 2020 21:08:53: 15000000 INFO @ Sun, 21 Jun 2020 21:08:56: 19000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:09:02: 16000000 INFO @ Sun, 21 Jun 2020 21:09:04: 20000000 INFO @ Sun, 21 Jun 2020 21:09:08: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:09:08: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:09:08: #1 total tags in treatment: 20495765 INFO @ Sun, 21 Jun 2020 21:09:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:08: #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 21:09:09: #1 tags after filtering in treatment: 20495601 INFO @ Sun, 21 Jun 2020 21:09:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:10: 17000000 INFO @ Sun, 21 Jun 2020 21:09:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:11: #2 number of paired peaks: 5732 INFO @ Sun, 21 Jun 2020 21:09:11: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:11: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:11: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:11: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:11: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:09:11: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:09:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.10_model.r WARNING @ Sun, 21 Jun 2020 21:09:11: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:09:11: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Sun, 21 Jun 2020 21:09:11: #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 21:09:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:18: 18000000 INFO @ Sun, 21 Jun 2020 21:09:25: 19000000 INFO @ Sun, 21 Jun 2020 21:09:33: 20000000 INFO @ Sun, 21 Jun 2020 21:09:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.05_summits.bed INFO @ Sun, 21 Jun 2020 21:09:36: Done! pass1 - making usageList (110 chroms): 2 millis pass2 - checking and writing primary data (12608 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:37: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 21:09:37: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 21:09:37: #1 total tags in treatment: 20495765 INFO @ Sun, 21 Jun 2020 21:09:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:09:37: #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 21:09:37: #1 tags after filtering in treatment: 20495601 INFO @ Sun, 21 Jun 2020 21:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:09:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:09:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:09:39: #2 number of paired peaks: 5732 INFO @ Sun, 21 Jun 2020 21:09:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:09:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:09:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:09:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:09:40: #2 predicted fragment length is 135 bps INFO @ Sun, 21 Jun 2020 21:09:40: #2 alternative fragment length(s) may be 135 bps INFO @ Sun, 21 Jun 2020 21:09:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.20_model.r WARNING @ Sun, 21 Jun 2020 21:09:40: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:09:40: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Sun, 21 Jun 2020 21:09:40: #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 21:09:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:09:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.10_summits.bed INFO @ Sun, 21 Jun 2020 21:10:23: Done! pass1 - making usageList (81 chroms): 2 millis pass2 - checking and writing primary data (10768 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:10:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315043/SRX4315043.20_summits.bed INFO @ Sun, 21 Jun 2020 21:10:50: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (8570 records, 4 fields): 12 millis CompletedMACS2peakCalling