[2024-01-24 13:40:33,302] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:33,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:33,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference
[2024-01-24 13:40:34,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:34,617] [INFO] Task started: Prodigal
[2024-01-24 13:40:34,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a279401-43bd-42b0-9523-aad4e8e56941/GCF_016134045.1_ASM1613404v1_genomic.fna.gz | prodigal -d GCF_016134045.1_ASM1613404v1_genomic.fna/cds.fna -a GCF_016134045.1_ASM1613404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:46,295] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:46,295] [INFO] Task started: HMMsearch
[2024-01-24 13:40:46,295] [INFO] Running command: hmmsearch --tblout GCF_016134045.1_ASM1613404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference/reference_markers.hmm GCF_016134045.1_ASM1613404v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:46,634] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:46,636] [INFO] Found 6/6 markers.
[2024-01-24 13:40:46,673] [INFO] Query marker FASTA was written to GCF_016134045.1_ASM1613404v1_genomic.fna/markers.fasta
[2024-01-24 13:40:46,673] [INFO] Task started: Blastn
[2024-01-24 13:40:46,673] [INFO] Running command: blastn -query GCF_016134045.1_ASM1613404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference/reference_markers.fasta -out GCF_016134045.1_ASM1613404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:47,588] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:47,591] [INFO] Selected 23 target genomes.
[2024-01-24 13:40:47,592] [INFO] Target genome list was writen to GCF_016134045.1_ASM1613404v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:47,614] [INFO] Task started: fastANI
[2024-01-24 13:40:47,614] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a279401-43bd-42b0-9523-aad4e8e56941/GCF_016134045.1_ASM1613404v1_genomic.fna.gz --refList GCF_016134045.1_ASM1613404v1_genomic.fna/target_genomes.txt --output GCF_016134045.1_ASM1613404v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:06,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:06,900] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:06,901] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:06,918] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:06,918] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:06,918] [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
Pelagovum pacificum	strain=SM1903	GCA_016134045.1	2588711	2588711	type	True	100.0	1361	1362	95	conclusive
Pelagovum pacificum	strain=SM1903	GCA_006363825.1	2588711	2588711	type	True	99.9964	1353	1362	95	conclusive
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.3427	611	1362	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.2842	599	1362	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	79.1576	548	1362	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.0186	553	1362	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.8211	500	1362	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.785	456	1362	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.7503	470	1362	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	78.7263	487	1362	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.5637	468	1362	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	78.3994	518	1362	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.34	446	1362	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.0969	392	1362	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.9859	374	1362	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.8716	423	1362	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.8362	332	1362	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.7494	319	1362	95	below_threshold
Rubellimicrobium aerolatum	strain=DSM 19297	GCA_017872975.1	490979	490979	type	True	77.6921	381	1362	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.5419	386	1362	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5278	354	1362	95	below_threshold
Pseudopuniceibacterium sediminis	strain=CY03	GCA_003575965.1	2211117	2211117	type	True	77.3159	307	1362	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	77.2166	294	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:06,920] [INFO] DFAST Taxonomy check result was written to GCF_016134045.1_ASM1613404v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:06,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:06,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:06,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference/checkm_data
[2024-01-24 13:41:06,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:06,965] [INFO] Task started: CheckM
[2024-01-24 13:41:06,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016134045.1_ASM1613404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016134045.1_ASM1613404v1_genomic.fna/checkm_input GCF_016134045.1_ASM1613404v1_genomic.fna/checkm_result
[2024-01-24 13:41:47,781] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:47,782] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,805] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:47,806] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:47,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016134045.1_ASM1613404v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:47,806] [INFO] Task started: Blastn
[2024-01-24 13:41:47,807] [INFO] Running command: blastn -query GCF_016134045.1_ASM1613404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg75f1bc4a-e4cf-4c10-a8c8-0bef820aefa0/dqc_reference/reference_markers_gtdb.fasta -out GCF_016134045.1_ASM1613404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:49,315] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:49,319] [INFO] Selected 20 target genomes.
[2024-01-24 13:41:49,319] [INFO] Target genome list was writen to GCF_016134045.1_ASM1613404v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:49,333] [INFO] Task started: fastANI
[2024-01-24 13:41:49,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a279401-43bd-42b0-9523-aad4e8e56941/GCF_016134045.1_ASM1613404v1_genomic.fna.gz --refList GCF_016134045.1_ASM1613404v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016134045.1_ASM1613404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:06,813] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:06,833] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:06,833] [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
GCF_016134045.1	s__Oceanicola pacificus_A	100.0	1361	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000153305.1	s__Oceanicola granulosus	81.0876	706	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	79.9869	605	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789055.1	s__Oceanicola lentulus	79.207	563	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172355.1	s__Oceanicola antarcticus	79.1704	606	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.024	550	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	78.7974	454	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	78.7279	489	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_002210105.1	s__Pseudooceanicola sp002210105	78.6493	457	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.5165	504	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	78.422	518	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCA_016806125.1	s__AWRV01 sp000504185	78.3888	470	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCF_015223355.1	s__Salipiger pacificus_B	78.3008	499	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116195.1	s__Salipiger pacificus	78.2328	501	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCA_003605175.1	s__IMCC34051 sp003605175	78.1393	432	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	77.8453	337	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	77.7827	379	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_003003095.1	s__Hasllibacter halocynthiae	77.7294	321	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Hasllibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.5461	387	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003575965.1	s__Pseudooceanicola sediminis	77.2967	309	1362	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.95	99.95	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:06,835] [INFO] GTDB search result was written to GCF_016134045.1_ASM1613404v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:06,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:06,841] [INFO] DFAST_QC result json was written to GCF_016134045.1_ASM1613404v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:06,841] [INFO] DFAST_QC completed!
[2024-01-24 13:42:06,841] [INFO] Total running time: 0h1m34s