Job ID = 6457034 SRX = SRX4315056 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:18:54 prefetch.2.10.7: 1) Downloading 'SRR7444517'... 2020-06-21T11:18:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:54 prefetch.2.10.7: 'SRR7444517' is valid 2020-06-21T11:20:54 prefetch.2.10.7: 1) 'SRR7444517' was downloaded successfully 2020-06-21T11:21:31 prefetch.2.10.7: 'SRR7444517' has 7 unresolved dependencies 2020-06-21T11:21:31 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:21:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:21:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:21:47 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:21:47 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:21:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:05 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:22:05 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:22:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:17 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:22:17 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:22:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:35 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:22:35 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:22:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:22:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:22:57 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:22:57 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:22:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:15 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:23:15 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:23:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:23:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:23:28 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 22674832 spots for SRR7444517/SRR7444517.sra Written 22674832 spots for SRR7444517/SRR7444517.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: 00:04:53 22674832 reads; of these: 22674832 (100.00%) were unpaired; of these: 6382 (0.03%) aligned 0 times 20477093 (90.31%) aligned exactly 1 time 2191357 (9.66%) aligned >1 times 99.97% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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] 8640392 / 22668450 = 0.3812 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 20:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.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 20:35:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:11: 1000000 INFO @ Sun, 21 Jun 2020 20:35:16: 2000000 INFO @ Sun, 21 Jun 2020 20:35:22: 3000000 INFO @ Sun, 21 Jun 2020 20:35:27: 4000000 INFO @ Sun, 21 Jun 2020 20:35:33: 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 20:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.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 20:35:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:38: 6000000 INFO @ Sun, 21 Jun 2020 20:35:41: 1000000 INFO @ Sun, 21 Jun 2020 20:35:44: 7000000 INFO @ Sun, 21 Jun 2020 20:35:47: 2000000 INFO @ Sun, 21 Jun 2020 20:35:50: 8000000 INFO @ Sun, 21 Jun 2020 20:35:53: 3000000 INFO @ Sun, 21 Jun 2020 20:35:56: 9000000 INFO @ Sun, 21 Jun 2020 20:35:59: 4000000 INFO @ Sun, 21 Jun 2020 20:36:02: 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 @ Sun, 21 Jun 2020 20:36:05: 5000000 INFO @ Sun, 21 Jun 2020 20:36:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.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 20:36:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:08: 11000000 INFO @ Sun, 21 Jun 2020 20:36:11: 6000000 INFO @ Sun, 21 Jun 2020 20:36:11: 1000000 INFO @ Sun, 21 Jun 2020 20:36:14: 12000000 INFO @ Sun, 21 Jun 2020 20:36:17: 7000000 INFO @ Sun, 21 Jun 2020 20:36:18: 2000000 INFO @ Sun, 21 Jun 2020 20:36:20: 13000000 INFO @ Sun, 21 Jun 2020 20:36:23: 8000000 INFO @ Sun, 21 Jun 2020 20:36:24: 3000000 INFO @ Sun, 21 Jun 2020 20:36:26: 14000000 INFO @ Sun, 21 Jun 2020 20:36:26: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:36:26: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:36:26: #1 total tags in treatment: 14028058 INFO @ Sun, 21 Jun 2020 20:36:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:26: #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 20:36:27: #1 tags after filtering in treatment: 14027902 INFO @ Sun, 21 Jun 2020 20:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:28: #2 number of paired peaks: 4073 INFO @ Sun, 21 Jun 2020 20:36:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:28: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 20:36:28: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 20:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.05_model.r WARNING @ Sun, 21 Jun 2020 20:36:28: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:36:28: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sun, 21 Jun 2020 20:36:28: #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 20:36:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:36:28: 9000000 INFO @ Sun, 21 Jun 2020 20:36:30: 4000000 INFO @ Sun, 21 Jun 2020 20:36:34: 10000000 INFO @ Sun, 21 Jun 2020 20:36:35: 5000000 INFO @ Sun, 21 Jun 2020 20:36:40: 11000000 INFO @ Sun, 21 Jun 2020 20:36:41: 6000000 INFO @ Sun, 21 Jun 2020 20:36:46: 12000000 INFO @ Sun, 21 Jun 2020 20:36:47: 7000000 INFO @ Sun, 21 Jun 2020 20:36:52: 13000000 INFO @ Sun, 21 Jun 2020 20:36:53: 8000000 INFO @ Sun, 21 Jun 2020 20:36:58: 14000000 INFO @ Sun, 21 Jun 2020 20:36:58: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:36:58: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:36:58: #1 total tags in treatment: 14028058 INFO @ Sun, 21 Jun 2020 20:36:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:58: #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 20:36:59: 9000000 INFO @ Sun, 21 Jun 2020 20:36:59: #1 tags after filtering in treatment: 14027902 INFO @ Sun, 21 Jun 2020 20:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:00: #2 number of paired peaks: 4073 INFO @ Sun, 21 Jun 2020 20:37:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:00: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 20:37:00: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 20:37:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.10_model.r WARNING @ Sun, 21 Jun 2020 20:37:00: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:00: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sun, 21 Jun 2020 20:37:00: #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 20:37:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:04: 10000000 INFO @ Sun, 21 Jun 2020 20:37:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:37:16: 12000000 INFO @ Sun, 21 Jun 2020 20:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.05_summits.bed INFO @ Sun, 21 Jun 2020 20:37:19: Done! pass1 - making usageList (122 chroms): 2 millis pass2 - checking and writing primary data (10133 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:21: 13000000 INFO @ Sun, 21 Jun 2020 20:37:27: 14000000 INFO @ Sun, 21 Jun 2020 20:37:27: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:37:27: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:37:27: #1 total tags in treatment: 14028058 INFO @ Sun, 21 Jun 2020 20:37:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:27: #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 20:37:27: #1 tags after filtering in treatment: 14027902 INFO @ Sun, 21 Jun 2020 20:37:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:29: #2 number of paired peaks: 4073 INFO @ Sun, 21 Jun 2020 20:37:29: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:29: #2 predicted fragment length is 130 bps INFO @ Sun, 21 Jun 2020 20:37:29: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 21 Jun 2020 20:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.20_model.r WARNING @ Sun, 21 Jun 2020 20:37:29: #2 Since the d (130) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:29: #2 You may need to consider one of the other alternative d(s): 130 WARNING @ Sun, 21 Jun 2020 20:37:29: #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 20:37:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.10_summits.bed INFO @ Sun, 21 Jun 2020 20:37:50: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (8112 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315056/SRX4315056.20_summits.bed INFO @ Sun, 21 Jun 2020 20:38:19: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (5875 records, 4 fields): 9 millis CompletedMACS2peakCalling