Job ID = 6457015 SRX = SRX4315038 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:23:09 prefetch.2.10.7: 1) Downloading 'SRR7444499'... 2020-06-21T11:23:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:24:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:24:10 prefetch.2.10.7: 'SRR7444499' is valid 2020-06-21T11:24:10 prefetch.2.10.7: 1) 'SRR7444499' was downloaded successfully 2020-06-21T11:24:48 prefetch.2.10.7: 'SRR7444499' has 7 unresolved dependencies 2020-06-21T11:24:48 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.5?vdb-ctx=refseq'... 2020-06-21T11:24:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:06 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:25:06 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.6?vdb-ctx=refseq'... 2020-06-21T11:25:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:23 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.6?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:25:23 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.4?vdb-ctx=refseq'... 2020-06-21T11:25:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:36 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:25:36 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.5?vdb-ctx=refseq'... 2020-06-21T11:25:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:25:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:25:54 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:25:54 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.3?vdb-ctx=refseq'... 2020-06-21T11:25:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:15 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:26:15 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.5?vdb-ctx=refseq'... 2020-06-21T11:26:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:34 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T11:26:34 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CP007106.1?vdb-ctx=refseq'... 2020-06-21T11:26:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:26:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:26:48 prefetch.2.10.7: 8) 'ncbi-acc:CP007106.1?vdb-ctx=refseq' was downloaded successfully Read 8793811 spots for SRR7444499/SRR7444499.sra Written 8793811 spots for SRR7444499/SRR7444499.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: 00:02:14 8793811 reads; of these: 8793811 (100.00%) were unpaired; of these: 4260 (0.05%) aligned 0 times 7851955 (89.29%) aligned exactly 1 time 937596 (10.66%) aligned >1 times 99.95% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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_rmdupse_core] 5205432 / 8789551 = 0.5922 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 20:32:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.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 20:32:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:32:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:32:19: 1000000 INFO @ Sun, 21 Jun 2020 20:32:27: 2000000 INFO @ Sun, 21 Jun 2020 20:32:36: 3000000 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 20:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.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 20:32:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:32:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:32:42: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:32:42: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:32:42: #1 total tags in treatment: 3584119 INFO @ Sun, 21 Jun 2020 20:32:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:32:42: #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 20:32:42: #1 tags after filtering in treatment: 3583784 INFO @ Sun, 21 Jun 2020 20:32:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:32:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:32:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:32:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:32:43: #2 number of paired peaks: 6498 INFO @ Sun, 21 Jun 2020 20:32:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:32:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:32:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:32:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:32:43: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 20:32:43: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 20:32:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.05_model.r WARNING @ Sun, 21 Jun 2020 20:32:43: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:32:43: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sun, 21 Jun 2020 20:32:43: #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 20:32:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:32:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:32:47: 1000000 INFO @ Sun, 21 Jun 2020 20:32:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:32:54: 2000000 INFO @ Sun, 21 Jun 2020 20:32:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:32:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:32:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.05_summits.bed INFO @ Sun, 21 Jun 2020 20:32:59: Done! pass1 - making usageList (122 chroms): 2 millis pass2 - checking and writing primary data (8289 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:33:01: 3000000 INFO @ Sun, 21 Jun 2020 20:33:05: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:33:05: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:33:05: #1 total tags in treatment: 3584119 INFO @ Sun, 21 Jun 2020 20:33:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:05: #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 20:33:06: #1 tags after filtering in treatment: 3583784 INFO @ Sun, 21 Jun 2020 20:33:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:06: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:06: #2 number of paired peaks: 6498 INFO @ Sun, 21 Jun 2020 20:33:06: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:06: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:06: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 20:33:06: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 20:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.10_model.r WARNING @ Sun, 21 Jun 2020 20:33:06: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:06: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sun, 21 Jun 2020 20:33:06: #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 20:33:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:06: #3 Pre-compute pvalue-qvalue table... 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 20:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.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 20:33:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:33:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:33:16: 1000000 INFO @ Sun, 21 Jun 2020 20:33:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:23: 2000000 INFO @ Sun, 21 Jun 2020 20:33:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.10_summits.bed INFO @ Sun, 21 Jun 2020 20:33:23: Done! pass1 - making usageList (85 chroms): 2 millis pass2 - checking and writing primary data (5924 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:33:30: 3000000 INFO @ Sun, 21 Jun 2020 20:33:34: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 20:33:34: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 20:33:34: #1 total tags in treatment: 3584119 INFO @ Sun, 21 Jun 2020 20:33:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:33:34: #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 20:33:35: #1 tags after filtering in treatment: 3583784 INFO @ Sun, 21 Jun 2020 20:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:33:35: #1 finished! INFO @ Sun, 21 Jun 2020 20:33:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:33:35: #2 number of paired peaks: 6498 INFO @ Sun, 21 Jun 2020 20:33:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:33:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:33:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:33:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:33:35: #2 predicted fragment length is 128 bps INFO @ Sun, 21 Jun 2020 20:33:35: #2 alternative fragment length(s) may be 128 bps INFO @ Sun, 21 Jun 2020 20:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.20_model.r WARNING @ Sun, 21 Jun 2020 20:33:35: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:33:35: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Sun, 21 Jun 2020 20:33:35: #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 20:33:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:33:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:33:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4315038/SRX4315038.20_summits.bed INFO @ Sun, 21 Jun 2020 20:33:52: Done! pass1 - making usageList (58 chroms): 1 millis pass2 - checking and writing primary data (3912 records, 4 fields): 8 millis CompletedMACS2peakCalling