[2023-06-27 04:25:05,064] [INFO] DFAST_QC pipeline started.
[2023-06-27 04:25:05,066] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 04:25:05,066] [INFO] DQC Reference Directory: /var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference
[2023-06-27 04:25:07,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 04:25:07,100] [INFO] Task started: Prodigal
[2023-06-27 04:25:07,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg2af668cb-0cce-48d3-848c-808ba9cdc6d2/GCA_026169335.1_ASM2616933v1_genomic.fna.gz | prodigal -d GCA_026169335.1_ASM2616933v1_genomic.fna/cds.fna -a GCA_026169335.1_ASM2616933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 04:25:11,501] [INFO] Task succeeded: Prodigal
[2023-06-27 04:25:11,502] [INFO] Task started: HMMsearch
[2023-06-27 04:25:11,502] [INFO] Running command: hmmsearch --tblout GCA_026169335.1_ASM2616933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference/reference_markers.hmm GCA_026169335.1_ASM2616933v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 04:25:11,736] [INFO] Task succeeded: HMMsearch
[2023-06-27 04:25:11,737] [INFO] Found 6/6 markers.
[2023-06-27 04:25:11,768] [INFO] Query marker FASTA was written to GCA_026169335.1_ASM2616933v1_genomic.fna/markers.fasta
[2023-06-27 04:25:11,768] [INFO] Task started: Blastn
[2023-06-27 04:25:11,768] [INFO] Running command: blastn -query GCA_026169335.1_ASM2616933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference/reference_markers.fasta -out GCA_026169335.1_ASM2616933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:25:12,369] [INFO] Task succeeded: Blastn
[2023-06-27 04:25:12,379] [INFO] Selected 22 target genomes.
[2023-06-27 04:25:12,379] [INFO] Target genome list was writen to GCA_026169335.1_ASM2616933v1_genomic.fna/target_genomes.txt
[2023-06-27 04:25:12,385] [INFO] Task started: fastANI
[2023-06-27 04:25:12,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg2af668cb-0cce-48d3-848c-808ba9cdc6d2/GCA_026169335.1_ASM2616933v1_genomic.fna.gz --refList GCA_026169335.1_ASM2616933v1_genomic.fna/target_genomes.txt --output GCA_026169335.1_ASM2616933v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 04:25:23,552] [INFO] Task succeeded: fastANI
[2023-06-27 04:25:23,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 04:25:23,553] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 04:25:23,576] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-06-27 04:25:23,576] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 04:25:23,577] [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
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	99.1311	529	575	95	conclusive
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.8556	142	575	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.7746	143	575	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.585	75	575	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.5737	143	575	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	77.5411	145	575	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	77.3225	99	575	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.3153	100	575	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.2345	123	575	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.2207	110	575	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.2003	58	575	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.1901	109	575	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	77.1768	59	575	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	76.8035	64	575	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	76.7602	64	575	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	76.1966	55	575	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 04:25:23,581] [INFO] DFAST Taxonomy check result was written to GCA_026169335.1_ASM2616933v1_genomic.fna/tc_result.tsv
[2023-06-27 04:25:23,582] [INFO] ===== Taxonomy check completed =====
[2023-06-27 04:25:23,582] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 04:25:23,582] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference/checkm_data
[2023-06-27 04:25:23,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 04:25:23,613] [INFO] Task started: CheckM
[2023-06-27 04:25:23,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026169335.1_ASM2616933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026169335.1_ASM2616933v1_genomic.fna/checkm_input GCA_026169335.1_ASM2616933v1_genomic.fna/checkm_result
[2023-06-27 04:25:44,122] [INFO] Task succeeded: CheckM
[2023-06-27 04:25:44,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.94%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 04:25:44,144] [INFO] ===== Completeness check finished =====
[2023-06-27 04:25:44,144] [INFO] ===== Start GTDB Search =====
[2023-06-27 04:25:44,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026169335.1_ASM2616933v1_genomic.fna/markers.fasta)
[2023-06-27 04:25:44,145] [INFO] Task started: Blastn
[2023-06-27 04:25:44,145] [INFO] Running command: blastn -query GCA_026169335.1_ASM2616933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4691cbd7-0141-423a-9ae1-ecc6396ad67d/dqc_reference/reference_markers_gtdb.fasta -out GCA_026169335.1_ASM2616933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 04:25:44,965] [INFO] Task succeeded: Blastn
[2023-06-27 04:25:44,970] [INFO] Selected 20 target genomes.
[2023-06-27 04:25:44,971] [INFO] Target genome list was writen to GCA_026169335.1_ASM2616933v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 04:25:44,982] [INFO] Task started: fastANI
[2023-06-27 04:25:44,982] [INFO] Running command: fastANI --query /var/lib/cwl/stg2af668cb-0cce-48d3-848c-808ba9cdc6d2/GCA_026169335.1_ASM2616933v1_genomic.fna.gz --refList GCA_026169335.1_ASM2616933v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026169335.1_ASM2616933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 04:25:55,531] [INFO] Task succeeded: fastANI
[2023-06-27 04:25:55,547] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 04:25:55,547] [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_900240315.1	s__Dorea_B phocaeensis	99.1311	529	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	conclusive
GCA_000433535.1	s__CAG-317 sp000433535	79.309	172	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCA_900543415.1	s__CAG-317 sp900543415	79.2421	168	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	97.35	95.87	0.87	0.78	4	-
GCF_003435815.1	s__CAG-317 sp000433215	77.8153	140	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCF_000154065.1	s__Dorea_A longicatena	77.7746	143	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCA_000509125.1	s__Clostridium_AP sp000509125	77.7701	143	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.12	98.62	0.95	0.91	5	-
GCA_905203555.1	s__Schaedlerella sp905203555	77.7298	81	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295505.1	s__Dorea_A sp016295505	77.717	125	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578495.1	s__CAG-317 sp910578495	77.6842	144	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295125.1	s__Clostridium_AP scindens	77.5411	145	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.44	99.12	0.90	0.78	13	-
GCA_900550865.1	s__Dorea_A sp900550865	77.5171	130	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584615.1	s__MD308 sp910584615	77.0185	107	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575605.1	s__UBA7109 sp910575605	76.853	109	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.27	99.27	0.93	0.93	2	-
GCF_001028025.1	s__Muricomes fissicatena_A	76.8412	56	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
GCF_000155205.1	s__Mediterraneibacter lactaris	76.7659	65	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.88	98.36	0.88	0.80	12	-
GCF_003574295.1	s__Mediterraneibacter_A butyricigenes	76.4328	73	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter_A	95.0	98.15	98.07	0.82	0.80	5	-
GCA_900550235.1	s__Faecalimonas sp900550235	76.344	59	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774255.1	s__Schaedlerella sp009774255	76.2421	51	575	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 04:25:55,549] [INFO] GTDB search result was written to GCA_026169335.1_ASM2616933v1_genomic.fna/result_gtdb.tsv
[2023-06-27 04:25:55,550] [INFO] ===== GTDB Search completed =====
[2023-06-27 04:25:55,554] [INFO] DFAST_QC result json was written to GCA_026169335.1_ASM2616933v1_genomic.fna/dqc_result.json
[2023-06-27 04:25:55,555] [INFO] DFAST_QC completed!
[2023-06-27 04:25:55,555] [INFO] Total running time: 0h0m50s