[2024-01-24 13:28:25,510] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,511] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,512] [INFO] DQC Reference Directory: /var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference
[2024-01-24 13:28:26,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:26,839] [INFO] Task started: Prodigal
[2024-01-24 13:28:26,839] [INFO] Running command: gunzip -c /var/lib/cwl/stg89790b4e-cdb5-480b-a666-d6605b88db02/GCF_000233955.1_ASM23395v1_genomic.fna.gz | prodigal -d GCF_000233955.1_ASM23395v1_genomic.fna/cds.fna -a GCF_000233955.1_ASM23395v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:54,982] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:54,982] [INFO] Task started: HMMsearch
[2024-01-24 13:28:54,982] [INFO] Running command: hmmsearch --tblout GCF_000233955.1_ASM23395v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference/reference_markers.hmm GCF_000233955.1_ASM23395v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:55,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:55,278] [INFO] Found 6/6 markers.
[2024-01-24 13:28:55,315] [INFO] Query marker FASTA was written to GCF_000233955.1_ASM23395v1_genomic.fna/markers.fasta
[2024-01-24 13:28:55,316] [INFO] Task started: Blastn
[2024-01-24 13:28:55,316] [INFO] Running command: blastn -query GCF_000233955.1_ASM23395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference/reference_markers.fasta -out GCF_000233955.1_ASM23395v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:55,956] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:55,960] [INFO] Selected 28 target genomes.
[2024-01-24 13:28:55,960] [INFO] Target genome list was writen to GCF_000233955.1_ASM23395v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:55,987] [INFO] Task started: fastANI
[2024-01-24 13:28:55,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg89790b4e-cdb5-480b-a666-d6605b88db02/GCF_000233955.1_ASM23395v1_genomic.fna.gz --refList GCF_000233955.1_ASM23395v1_genomic.fna/target_genomes.txt --output GCF_000233955.1_ASM23395v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:12,748] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:12,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:12,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:12,765] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:12,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:12,766] [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
Paraprevotella clara	strain=YIT 11840	GCA_000233955.1	454154	454154	type	True	100.0	1360	1362	95	conclusive
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	92.1981	985	1362	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	81.4371	82	1362	95	below_threshold
Phocaeicola sartorii	strain=DSM 21941	GCA_024622025.1	671267	671267	type	True	81.0133	102	1362	95	below_threshold
Bacteroides faecichinchillae	strain=DSM 26883	GCA_900129065.1	871325	871325	type	True	79.9958	68	1362	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	79.9343	97	1362	95	below_threshold
Bacteroides caecimuris	strain=I48	GCA_023277905.1	1796613	1796613	type	True	79.5821	100	1362	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	78.7573	88	1362	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	78.5101	94	1362	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	78.478	103	1362	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	78.4509	102	1362	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	78.45	101	1362	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	78.2807	94	1362	95	below_threshold
Phocaeicola salanitronis	strain=DSM 18170	GCA_000190575.1	376805	376805	type	True	77.9634	108	1362	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	77.3579	61	1362	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	77.3298	84	1362	95	below_threshold
Phocaeicola faecium	strain=Sa1YUN3	GCA_014837055.1	2762213	2762213	type	True	77.2723	81	1362	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	77.1969	83	1362	95	below_threshold
Bacteroides helcogenes	strain=P 36-108	GCA_000186225.1	290053	290053	type	True	77.0553	73	1362	95	below_threshold
Bacteroides ovatus	strain=ATCC 8483	GCA_025146775.1	28116	28116	suspected-type	True	77.0229	61	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:12,767] [INFO] DFAST Taxonomy check result was written to GCF_000233955.1_ASM23395v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:12,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:12,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:12,768] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference/checkm_data
[2024-01-24 13:29:12,769] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:12,810] [INFO] Task started: CheckM
[2024-01-24 13:29:12,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000233955.1_ASM23395v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000233955.1_ASM23395v1_genomic.fna/checkm_input GCF_000233955.1_ASM23395v1_genomic.fna/checkm_result
[2024-01-24 13:30:23,587] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:23,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:23,609] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:23,609] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:23,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000233955.1_ASM23395v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:23,610] [INFO] Task started: Blastn
[2024-01-24 13:30:23,610] [INFO] Running command: blastn -query GCF_000233955.1_ASM23395v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119379d7-a48d-4221-94d9-f760f69a5917/dqc_reference/reference_markers_gtdb.fasta -out GCF_000233955.1_ASM23395v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:24,423] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:24,427] [INFO] Selected 18 target genomes.
[2024-01-24 13:30:24,427] [INFO] Target genome list was writen to GCF_000233955.1_ASM23395v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:24,449] [INFO] Task started: fastANI
[2024-01-24 13:30:24,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg89790b4e-cdb5-480b-a666-d6605b88db02/GCF_000233955.1_ASM23395v1_genomic.fna.gz --refList GCF_000233955.1_ASM23395v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000233955.1_ASM23395v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:34,730] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:34,744] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:34,744] [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_000233955.1	s__Paraprevotella clara	100.0	1360	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	97.73	97.27	0.87	0.80	9	conclusive
GCF_000205165.1	s__Paraprevotella xylaniphila	92.2342	983	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.99	98.53	0.93	0.88	5	-
GCA_900760455.1	s__Paraprevotella sp900760455	79.1869	180	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	96.69	96.51	0.74	0.73	3	-
GCF_003477995.1	s__Paraprevotella sp003477995	79.162	177	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.53	97.92	0.95	0.91	5	-
GCA_910586505.1	s__Paraprevotella sp910586505	79.1455	386	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586915.1	s__Bacteroides sp910586915	79.079	82	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513195.1	s__Bacteroides timonensis	78.7838	74	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548345.1	s__Paraprevotella sp900548345	78.1602	270	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_017937925.1	s__Paraprevotella sp017937925	77.9278	99	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.10	97.94	0.89	0.89	3	-
GCA_900546665.1	s__Paraprevotella stercorigallinarum	77.5341	150	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	99.24	99.20	0.80	0.74	3	-
GCA_905214795.1	s__Paraprevotella sp905214795	77.0437	128	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:34,745] [INFO] GTDB search result was written to GCF_000233955.1_ASM23395v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:34,746] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:34,749] [INFO] DFAST_QC result json was written to GCF_000233955.1_ASM23395v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:34,749] [INFO] DFAST_QC completed!
[2024-01-24 13:30:34,749] [INFO] Total running time: 0h2m9s