[2023-06-28 19:48:04,319] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:04,321] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:04,321] [INFO] DQC Reference Directory: /var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference
[2023-06-28 19:48:05,627] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:05,628] [INFO] Task started: Prodigal
[2023-06-28 19:48:05,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg155bb1f0-e5f3-4810-9d75-9116c2ea990d/GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:16,504] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:16,505] [INFO] Task started: HMMsearch
[2023-06-28 19:48:16,505] [INFO] Running command: hmmsearch --tblout GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference/reference_markers.hmm GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:16,787] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:16,789] [INFO] Found 6/6 markers.
[2023-06-28 19:48:16,825] [INFO] Query marker FASTA was written to GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 19:48:16,825] [INFO] Task started: Blastn
[2023-06-28 19:48:16,825] [INFO] Running command: blastn -query GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference/reference_markers.fasta -out GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:17,682] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:17,686] [INFO] Selected 13 target genomes.
[2023-06-28 19:48:17,687] [INFO] Target genome list was writen to GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 19:48:17,702] [INFO] Task started: fastANI
[2023-06-28 19:48:17,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg155bb1f0-e5f3-4810-9d75-9116c2ea990d/GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:48:27,817] [INFO] Task succeeded: fastANI
[2023-06-28 19:48:27,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:48:27,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:48:27,833] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:48:27,834] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:48:27,834] [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
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	94.5469	977	1165	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	81.8012	689	1165	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	81.4787	645	1165	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	80.6678	642	1165	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.4588	574	1165	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	79.3044	420	1165	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.3965	325	1165	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	78.2664	351	1165	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	78.2452	360	1165	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.161	316	1165	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.43	200	1165	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.9581	75	1165	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	75.8102	54	1165	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:48:27,836] [INFO] DFAST Taxonomy check result was written to GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 19:48:27,836] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:48:27,837] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:48:27,837] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference/checkm_data
[2023-06-28 19:48:27,838] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:48:27,875] [INFO] Task started: CheckM
[2023-06-28 19:48:27,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 19:49:03,959] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:03,960] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.99%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:03,981] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:03,981] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:03,982] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 19:49:03,982] [INFO] Task started: Blastn
[2023-06-28 19:49:03,982] [INFO] Running command: blastn -query GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc35cc917-4938-45c7-be90-903900db689e/dqc_reference/reference_markers_gtdb.fasta -out GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:05,471] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:05,476] [INFO] Selected 10 target genomes.
[2023-06-28 19:49:05,477] [INFO] Target genome list was writen to GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:05,505] [INFO] Task started: fastANI
[2023-06-28 19:49:05,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg155bb1f0-e5f3-4810-9d75-9116c2ea990d/GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:14,318] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:14,335] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:49:14,336] [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_002706085.1	s__Alcanivorax sp002706085	99.6769	1091	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.88	0.86	0.86	2	conclusive
GCF_003597125.1	s__Alcanivorax profundi	94.5469	977	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCA_017794965.1	s__Alcanivorax sp017794965	82.3707	733	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	81.8232	687	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882945.1	s__Alcanivorax sp009882945	81.5049	663	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009601165.1	s__Alcanivorax sediminis	81.485	644	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756655.1	s__Alcanivorax jadensis	80.7164	637	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_900107995.1	s__Alcanivorax sp900107995	80.6507	672	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.4586	574	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762765.1	s__Alcanivorax sp014762765	80.3683	568	1165	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:14,345] [INFO] GTDB search result was written to GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:14,346] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:14,351] [INFO] DFAST_QC result json was written to GCA_913044005.1_ERR599044_bin.36_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 19:49:14,351] [INFO] DFAST_QC completed!
[2023-06-28 19:49:14,351] [INFO] Total running time: 0h1m10s