[2024-01-25 18:55:35,583] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:55:35,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:55:35,585] [INFO] DQC Reference Directory: /var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference
[2024-01-25 18:55:36,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:55:36,744] [INFO] Task started: Prodigal
[2024-01-25 18:55:36,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg245aac86-410c-455e-97af-f1157989e04c/GCF_025150245.1_ASM2515024v1_genomic.fna.gz | prodigal -d GCF_025150245.1_ASM2515024v1_genomic.fna/cds.fna -a GCF_025150245.1_ASM2515024v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:55:43,564] [INFO] Task succeeded: Prodigal
[2024-01-25 18:55:43,565] [INFO] Task started: HMMsearch
[2024-01-25 18:55:43,565] [INFO] Running command: hmmsearch --tblout GCF_025150245.1_ASM2515024v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference/reference_markers.hmm GCF_025150245.1_ASM2515024v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:55:43,781] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:55:43,782] [INFO] Found 6/6 markers.
[2024-01-25 18:55:43,807] [INFO] Query marker FASTA was written to GCF_025150245.1_ASM2515024v1_genomic.fna/markers.fasta
[2024-01-25 18:55:43,807] [INFO] Task started: Blastn
[2024-01-25 18:55:43,807] [INFO] Running command: blastn -query GCF_025150245.1_ASM2515024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference/reference_markers.fasta -out GCF_025150245.1_ASM2515024v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:55:44,401] [INFO] Task succeeded: Blastn
[2024-01-25 18:55:44,404] [INFO] Selected 17 target genomes.
[2024-01-25 18:55:44,404] [INFO] Target genome list was writen to GCF_025150245.1_ASM2515024v1_genomic.fna/target_genomes.txt
[2024-01-25 18:55:44,413] [INFO] Task started: fastANI
[2024-01-25 18:55:44,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg245aac86-410c-455e-97af-f1157989e04c/GCF_025150245.1_ASM2515024v1_genomic.fna.gz --refList GCF_025150245.1_ASM2515024v1_genomic.fna/target_genomes.txt --output GCF_025150245.1_ASM2515024v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:54,163] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:54,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:54,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:54,178] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:55:54,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:54,179] [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 formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	100.0	1062	1062	95	conclusive
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	99.992	1048	1062	95	conclusive
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	84.3815	284	1062	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	81.3215	190	1062	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	80.6989	300	1062	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	80.6931	185	1062	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	80.5265	140	1062	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	80.4823	181	1062	95	below_threshold
Suipraeoptans intestinalis	strain=68-1-5	GCA_009696485.1	2606628	2606628	type	True	80.3524	84	1062	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	80.3261	293	1062	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	80.1459	109	1062	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.9889	174	1062	95	below_threshold
Anaerostipes butyraticus	strain=JCM 17466	GCA_016586355.1	645466	645466	type	True	78.8218	69	1062	95	below_threshold
Aequitasia blattaphilus	strain=PAL113	GCA_024160205.1	2949332	2949332	type	True	78.2039	68	1062	95	below_threshold
Aequitasia blattaphilus	strain=PAL113	GCA_024721305.1	2949332	2949332	type	True	78.2039	68	1062	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.8287	94	1062	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:54,180] [INFO] DFAST Taxonomy check result was written to GCF_025150245.1_ASM2515024v1_genomic.fna/tc_result.tsv
[2024-01-25 18:55:54,181] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:54,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:54,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference/checkm_data
[2024-01-25 18:55:54,182] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:54,218] [INFO] Task started: CheckM
[2024-01-25 18:55:54,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025150245.1_ASM2515024v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025150245.1_ASM2515024v1_genomic.fna/checkm_input GCF_025150245.1_ASM2515024v1_genomic.fna/checkm_result
[2024-01-25 18:56:19,120] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:19,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:19,149] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:19,149] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:19,150] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025150245.1_ASM2515024v1_genomic.fna/markers.fasta)
[2024-01-25 18:56:19,150] [INFO] Task started: Blastn
[2024-01-25 18:56:19,150] [INFO] Running command: blastn -query GCF_025150245.1_ASM2515024v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg99e0de72-7700-4d80-8a88-c54db97bc426/dqc_reference/reference_markers_gtdb.fasta -out GCF_025150245.1_ASM2515024v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:20,197] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:20,202] [INFO] Selected 24 target genomes.
[2024-01-25 18:56:20,202] [INFO] Target genome list was writen to GCF_025150245.1_ASM2515024v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:20,239] [INFO] Task started: fastANI
[2024-01-25 18:56:20,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg245aac86-410c-455e-97af-f1157989e04c/GCF_025150245.1_ASM2515024v1_genomic.fna.gz --refList GCF_025150245.1_ASM2515024v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025150245.1_ASM2515024v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:33,923] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:33,935] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:33,936] [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_000169235.1	s__Dorea formicigenerans	99.992	1048	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea	95.0	97.68	96.97	0.80	0.73	43	conclusive
GCF_008121495.1	s__Ruminococcus_B gnavus	81.3636	183	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCF_003435815.1	s__CAG-317 sp000433215	81.3024	318	1062	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_001404875.1	s__Dorea_A longicatena_B	81.2608	315	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCF_000469345.1	s__Eubacterium_I ramulus	80.5694	139	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.54	98.22	0.85	0.78	13	-
GCF_000154065.1	s__Dorea_A longicatena	80.3261	293	1062	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	-
GCF_000153925.1	s__Mediterraneibacter torques	80.1988	108	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.42	99.19	0.88	0.82	25	-
GCF_004295125.1	s__Clostridium_AP scindens	80.0241	150	1062	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	-
GCF_000403455.2	s__Sporofaciens sp000403455	79.3912	145	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.91	98.91	0.91	0.91	2	-
GCA_910575605.1	s__UBA7109 sp910575605	79.3746	151	1062	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_900240315.1	s__Dorea_B phocaeensis	78.9889	174	1062	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	-
GCA_900550865.1	s__Dorea_A sp900550865	78.3225	223	1062	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	-
GCF_002159505.1	s__Mediterraneibacter ornithocaccae	78.2858	97	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	-
GCA_000509125.1	s__Clostridium_AP sp000509125	78.0959	118	1062	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_900546495.1	s__Eubacterium_I sp900546495	77.9041	120	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.94	99.87	0.93	0.88	3	-
GCF_016902415.1	s__Merdimonas massiliensis	77.6711	118	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	97.93	97.91	0.86	0.83	3	-
GCA_905216215.1	s__Bariatricus sp905216215	77.6216	123	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492335.1	s__UBA7109 sp002492335	77.5704	122	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	77.1157	71	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCA_910584615.1	s__MD308 sp910584615	76.9831	106	1062	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_019113645.1	s__Mediterraneibacter vanvlietii	76.8011	91	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.04	97.81	0.84	0.83	3	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	76.6007	73	1062	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:56:33,937] [INFO] GTDB search result was written to GCF_025150245.1_ASM2515024v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:33,937] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:33,940] [INFO] DFAST_QC result json was written to GCF_025150245.1_ASM2515024v1_genomic.fna/dqc_result.json
[2024-01-25 18:56:33,940] [INFO] DFAST_QC completed!
[2024-01-25 18:56:33,940] [INFO] Total running time: 0h0m58s