[2023-03-16 04:39:50,917] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:39:50,917] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:39:50,917] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference
[2023-03-16 04:39:55,305] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:39:55,306] [INFO] Task started: Prodigal
[2023-03-16 04:39:55,306] [INFO] Running command: cat /var/lib/cwl/stgdb715314-82fd-4ed2-a874-6afbf6017f1e/OceanDNA-b5298.fa | prodigal -d OceanDNA-b5298/cds.fna -a OceanDNA-b5298/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:40:18,001] [INFO] Task succeeded: Prodigal
[2023-03-16 04:40:18,001] [INFO] Task started: HMMsearch
[2023-03-16 04:40:18,001] [INFO] Running command: hmmsearch --tblout OceanDNA-b5298/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference/reference_markers.hmm OceanDNA-b5298/protein.faa > /dev/null
[2023-03-16 04:40:18,243] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:40:18,244] [INFO] Found 6/6 markers.
[2023-03-16 04:40:18,263] [INFO] Query marker FASTA was written to OceanDNA-b5298/markers.fasta
[2023-03-16 04:40:18,264] [INFO] Task started: Blastn
[2023-03-16 04:40:18,264] [INFO] Running command: blastn -query OceanDNA-b5298/markers.fasta -db /var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference/reference_markers.fasta -out OceanDNA-b5298/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:21,669] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:21,670] [INFO] Selected 26 target genomes.
[2023-03-16 04:40:21,670] [INFO] Target genome list was writen to OceanDNA-b5298/target_genomes.txt
[2023-03-16 04:40:21,684] [INFO] Task started: fastANI
[2023-03-16 04:40:21,684] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb715314-82fd-4ed2-a874-6afbf6017f1e/OceanDNA-b5298.fa --refList OceanDNA-b5298/target_genomes.txt --output OceanDNA-b5298/fastani_result.tsv --threads 1
[2023-03-16 04:40:36,303] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:36,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:40:36,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:40:36,310] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:40:36,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:40:36,310] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Fluviicola taffensis	strain=DSM 16823	GCA_000194605.1	191579	191579	type	True	76.5643	86	1064	95	below_threshold
Lishizhenia tianjinensis	strain=CGMCC 1.7005	GCA_900116425.1	477690	477690	type	True	76.5371	60	1064	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	76.1437	66	1064	95	below_threshold
Brumimicrobium mesophilum	strain=JCM 14063	GCA_003025005.1	392717	392717	type	True	75.9779	60	1064	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:40:36,311] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5298/tc_result.tsv
[2023-03-16 04:40:36,311] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:40:36,311] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:40:36,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference/checkm_data
[2023-03-16 04:40:36,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:40:36,316] [INFO] Task started: CheckM
[2023-03-16 04:40:36,316] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5298/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5298/checkm_input OceanDNA-b5298/checkm_result
[2023-03-16 04:41:34,056] [INFO] Task succeeded: CheckM
[2023-03-16 04:41:34,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:41:34,059] [INFO] ===== Completeness check finished =====
[2023-03-16 04:41:34,059] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:41:34,059] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5298/markers.fasta)
[2023-03-16 04:41:34,059] [INFO] Task started: Blastn
[2023-03-16 04:41:34,059] [INFO] Running command: blastn -query OceanDNA-b5298/markers.fasta -db /var/lib/cwl/stgd4e731b2-8acf-4f58-bf63-599f8d3b6b3b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5298/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:41:34,832] [INFO] Task succeeded: Blastn
[2023-03-16 04:41:34,833] [INFO] Selected 28 target genomes.
[2023-03-16 04:41:34,833] [INFO] Target genome list was writen to OceanDNA-b5298/target_genomes_gtdb.txt
[2023-03-16 04:41:34,933] [INFO] Task started: fastANI
[2023-03-16 04:41:34,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb715314-82fd-4ed2-a874-6afbf6017f1e/OceanDNA-b5298.fa --refList OceanDNA-b5298/target_genomes_gtdb.txt --output OceanDNA-b5298/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:41:47,917] [INFO] Task succeeded: fastANI
[2023-03-16 04:41:47,925] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:41:47,925] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002384725.1	s__UBA2040 sp002384725	77.7362	147	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA2040	95.0	99.28	99.28	0.79	0.79	2	-
GCA_002332715.1	s__UBA2040 sp002332715	77.6247	116	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA2040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402525.1	s__UBA4466 sp018402525	77.0821	65	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984635.1	s__M0103 sp017984635	77.0045	91	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018825925.1	s__UBA2040 sp018825925	76.9658	81	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA2040	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930085.1	s__M0103 sp903930085	76.875	54	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983675.1	s__Fluviicola sp017983675	76.7433	67	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	99.86	99.86	0.97	0.97	2	-
GCA_905182335.1	s__UBA4466 sp905182335	76.7325	52	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	99.88	99.88	0.98	0.98	2	-
GCA_018883325.1	s__UBA952 sp018883325	76.6094	92	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002483265.1	s__Fluviicola sp002483265	76.5961	69	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000194605.1	s__Fluviicola taffensis	76.5643	86	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Fluviicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480145.1	s__UBA4466 sp905480145	76.3945	61	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA4466	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885545.1	s__M0103 sp009885545	76.3793	79	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__M0103	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	76.1437	66	1064	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:41:47,925] [INFO] GTDB search result was written to OceanDNA-b5298/result_gtdb.tsv
[2023-03-16 04:41:47,925] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:41:47,927] [INFO] DFAST_QC result json was written to OceanDNA-b5298/dqc_result.json
[2023-03-16 04:41:47,927] [INFO] DFAST_QC completed!
[2023-03-16 04:41:47,927] [INFO] Total running time: 0h1m57s