[2023-03-16 04:31:43,752] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:31:43,752] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:31:43,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference
[2023-03-16 04:31:45,528] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:31:45,529] [INFO] Task started: Prodigal
[2023-03-16 04:31:45,529] [INFO] Running command: cat /var/lib/cwl/stg215807d5-fcc5-457e-8426-b0b858f325d0/OceanDNA-b36642.fa | prodigal -d OceanDNA-b36642/cds.fna -a OceanDNA-b36642/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:32:04,663] [INFO] Task succeeded: Prodigal
[2023-03-16 04:32:04,663] [INFO] Task started: HMMsearch
[2023-03-16 04:32:04,663] [INFO] Running command: hmmsearch --tblout OceanDNA-b36642/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference/reference_markers.hmm OceanDNA-b36642/protein.faa > /dev/null
[2023-03-16 04:32:04,883] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:32:04,883] [INFO] Found 6/6 markers.
[2023-03-16 04:32:04,902] [INFO] Query marker FASTA was written to OceanDNA-b36642/markers.fasta
[2023-03-16 04:32:04,903] [INFO] Task started: Blastn
[2023-03-16 04:32:04,903] [INFO] Running command: blastn -query OceanDNA-b36642/markers.fasta -db /var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference/reference_markers.fasta -out OceanDNA-b36642/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:32:05,674] [INFO] Task succeeded: Blastn
[2023-03-16 04:32:05,675] [INFO] Selected 23 target genomes.
[2023-03-16 04:32:05,675] [INFO] Target genome list was writen to OceanDNA-b36642/target_genomes.txt
[2023-03-16 04:32:05,690] [INFO] Task started: fastANI
[2023-03-16 04:32:05,690] [INFO] Running command: fastANI --query /var/lib/cwl/stg215807d5-fcc5-457e-8426-b0b858f325d0/OceanDNA-b36642.fa --refList OceanDNA-b36642/target_genomes.txt --output OceanDNA-b36642/fastani_result.tsv --threads 1
[2023-03-16 04:32:20,653] [INFO] Task succeeded: fastANI
[2023-03-16 04:32:20,654] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:32:20,654] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:32:20,665] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:32:20,665] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:32:20,665] [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 pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	77.4848	235	969	95	below_threshold
Alcanivorax indicus	strain=SW127	GCA_003259185.1	2202653	2202653	type	True	77.3771	216	969	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	77.1793	186	969	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	76.9659	161	969	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.9651	206	969	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	76.9288	194	969	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.9278	167	969	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	76.9093	154	969	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	76.8894	153	969	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	76.8036	201	969	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.7495	187	969	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	76.7481	157	969	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	76.4408	52	969	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	76.4238	159	969	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.4237	81	969	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.2535	79	969	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	76.1935	79	969	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	75.9436	63	969	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:32:20,665] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36642/tc_result.tsv
[2023-03-16 04:32:20,666] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:32:20,666] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:32:20,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference/checkm_data
[2023-03-16 04:32:20,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:32:20,772] [INFO] Task started: CheckM
[2023-03-16 04:32:20,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36642/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36642/checkm_input OceanDNA-b36642/checkm_result
[2023-03-16 04:33:10,737] [INFO] Task succeeded: CheckM
[2023-03-16 04:33:10,737] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:33:10,743] [INFO] ===== Completeness check finished =====
[2023-03-16 04:33:10,743] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:33:10,743] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36642/markers.fasta)
[2023-03-16 04:33:10,744] [INFO] Task started: Blastn
[2023-03-16 04:33:10,744] [INFO] Running command: blastn -query OceanDNA-b36642/markers.fasta -db /var/lib/cwl/stg8c78450c-56d4-4dab-83c3-f33871572e32/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36642/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:33:12,223] [INFO] Task succeeded: Blastn
[2023-03-16 04:33:12,224] [INFO] Selected 24 target genomes.
[2023-03-16 04:33:12,224] [INFO] Target genome list was writen to OceanDNA-b36642/target_genomes_gtdb.txt
[2023-03-16 04:33:12,249] [INFO] Task started: fastANI
[2023-03-16 04:33:12,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg215807d5-fcc5-457e-8426-b0b858f325d0/OceanDNA-b36642.fa --refList OceanDNA-b36642/target_genomes_gtdb.txt --output OceanDNA-b36642/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:33:26,316] [INFO] Task succeeded: fastANI
[2023-03-16 04:33:26,327] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:33:26,328] [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_002840115.1	s__PGZG01 sp002840115	79.0805	191	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__PGZG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299335.2	s__Alcanivorax_A pacificus	77.497	234	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259185.1	s__Alcanivorax_A indicus	77.3771	216	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009846755.1	s__Alcanivorax_A sp009846755	77.276	235	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003862375.1	s__Alcanivorax jadensis_A	77.2019	170	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_015356855.1	s__Alcanivorax venustensis	77.193	185	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCA_013823245.1	s__Alcanivorax_A sp013823245	77.1434	209	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733835.1	s__Alcanivorax sp002733835	77.0784	136	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906305.1	s__Alcanivorax marinus_B	77.0703	175	969	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	77.0661	164	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002864685.1	s__Alcanivorax mobilis	76.9659	161	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.57	98.57	0.96	0.96	2	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	76.9169	195	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCA_017794945.1	s__Alcanivorax sp009711585	76.8942	155	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_000300995.1	s__Alcanivorax hongdengensis	76.7917	202	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	76.7495	187	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_003597125.1	s__Alcanivorax profundi	76.7481	157	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCA_002706085.1	s__Alcanivorax sp002706085	76.7374	138	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.88	0.86	0.86	2	-
GCA_002726155.1	s__Alcanivorax sp002726155	76.5361	127	969	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	76.4111	160	969	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:33:26,330] [INFO] GTDB search result was written to OceanDNA-b36642/result_gtdb.tsv
[2023-03-16 04:33:26,336] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:33:26,342] [INFO] DFAST_QC result json was written to OceanDNA-b36642/dqc_result.json
[2023-03-16 04:33:26,342] [INFO] DFAST_QC completed!
[2023-03-16 04:33:26,342] [INFO] Total running time: 0h1m43s