[2024-01-24 15:18:51,885] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:51,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:51,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference
[2024-01-24 15:18:54,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:54,600] [INFO] Task started: Prodigal
[2024-01-24 15:18:54,602] [INFO] Running command: gunzip -c /var/lib/cwl/stg6ca6ff3d-8bc0-42d8-893c-390579184361/GCF_025567175.1_ASM2556717v1_genomic.fna.gz | prodigal -d GCF_025567175.1_ASM2556717v1_genomic.fna/cds.fna -a GCF_025567175.1_ASM2556717v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:02,230] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:02,231] [INFO] Task started: HMMsearch
[2024-01-24 15:19:02,231] [INFO] Running command: hmmsearch --tblout GCF_025567175.1_ASM2556717v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference/reference_markers.hmm GCF_025567175.1_ASM2556717v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:02,492] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:02,493] [INFO] Found 6/6 markers.
[2024-01-24 15:19:02,522] [INFO] Query marker FASTA was written to GCF_025567175.1_ASM2556717v1_genomic.fna/markers.fasta
[2024-01-24 15:19:02,522] [INFO] Task started: Blastn
[2024-01-24 15:19:02,522] [INFO] Running command: blastn -query GCF_025567175.1_ASM2556717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference/reference_markers.fasta -out GCF_025567175.1_ASM2556717v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:03,244] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:03,247] [INFO] Selected 17 target genomes.
[2024-01-24 15:19:03,248] [INFO] Target genome list was writen to GCF_025567175.1_ASM2556717v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:03,282] [INFO] Task started: fastANI
[2024-01-24 15:19:03,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca6ff3d-8bc0-42d8-893c-390579184361/GCF_025567175.1_ASM2556717v1_genomic.fna.gz --refList GCF_025567175.1_ASM2556717v1_genomic.fna/target_genomes.txt --output GCF_025567175.1_ASM2556717v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:12,083] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:12,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:12,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:12,100] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:12,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:12,100] [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
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	99.7795	928	962	95	conclusive
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.1268	195	962	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.0438	189	962	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	78.901	193	962	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.8556	194	962	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.3386	145	962	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.2783	153	962	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.1763	87	962	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	78.0145	175	962	95	below_threshold
Luxibacter massiliensis	strain=Marseille-P5551	GCA_900604355.1	2219695	2219695	type	True	77.7006	144	962	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.6681	90	962	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.531	106	962	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.456	149	962	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.4392	103	962	95	below_threshold
Sellimonas caecigallum	strain=SW451	GCA_019754295.1	2592333	2592333	type	True	77.1496	70	962	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:12,102] [INFO] DFAST Taxonomy check result was written to GCF_025567175.1_ASM2556717v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:12,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:12,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:12,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference/checkm_data
[2024-01-24 15:19:12,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:12,138] [INFO] Task started: CheckM
[2024-01-24 15:19:12,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567175.1_ASM2556717v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567175.1_ASM2556717v1_genomic.fna/checkm_input GCF_025567175.1_ASM2556717v1_genomic.fna/checkm_result
[2024-01-24 15:19:40,097] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:40,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:40,125] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:40,125] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:40,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567175.1_ASM2556717v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:40,126] [INFO] Task started: Blastn
[2024-01-24 15:19:40,127] [INFO] Running command: blastn -query GCF_025567175.1_ASM2556717v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg73b85598-8ba4-4b10-92ee-1fc8c7d41d57/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567175.1_ASM2556717v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:41,191] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:41,194] [INFO] Selected 22 target genomes.
[2024-01-24 15:19:41,194] [INFO] Target genome list was writen to GCF_025567175.1_ASM2556717v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:41,210] [INFO] Task started: fastANI
[2024-01-24 15:19:41,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ca6ff3d-8bc0-42d8-893c-390579184361/GCF_025567175.1_ASM2556717v1_genomic.fna.gz --refList GCF_025567175.1_ASM2556717v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567175.1_ASM2556717v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:54,197] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:54,213] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:54,213] [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_001487105.1	s__Mediterraneibacter massiliensis	99.7795	928	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.29	98.08	0.94	0.85	4	conclusive
GCF_014287475.1	s__Mediterraneibacter sp014287475	80.1088	506	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	96.03	96.03	0.75	0.75	2	-
GCF_008121495.1	s__Ruminococcus_B gnavus	79.1385	194	962	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	-
GCA_900765975.1	s__Schaedlerella sp900765975	78.6013	144	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.94	99.94	0.80	0.80	2	-
GCA_900541505.1	s__Mediterraneibacter sp900541505	78.5674	293	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.61	98.61	0.89	0.89	2	-
GCF_018228665.1	s__UBA9414 sp003458885	78.5099	96	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCF_000155205.1	s__Mediterraneibacter lactaris	78.3485	144	962	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_012524165.2	s__Muricomes sp012524165	77.9804	176	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001404335.1	s__Muricomes contortus_B	77.8481	162	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	98.80	98.64	0.86	0.83	8	-
GCA_910574195.1	s__Schaedlerella sp910574195	77.8435	118	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.97	99.97	0.98	0.98	2	-
GCF_015560805.1	s__Schaedlerella glycyrrhizinilytica_A	77.8349	194	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.33	97.63	0.90	0.83	10	-
GCF_016902345.1	s__Mediterraneibacter glycyrrhizinilyticus_A	77.8346	141	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001028025.1	s__Muricomes fissicatena_A	77.7915	167	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	99.01	99.01	0.90	0.90	3	-
GCA_904418845.1	s__Mediterraneibacter sp904418845	77.6591	119	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900751785.1	s__Mediterraneibacter faecigallinarum	77.4778	130	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.56	97.84	0.86	0.78	4	-
GCA_905203555.1	s__Schaedlerella sp905203555	77.4684	147	962	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_019119995.1	s__Mediterraneibacter faecavium	77.2671	144	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
GCA_019115385.1	s__Mediterraneibacter avicola	77.1029	115	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.73	98.73	0.86	0.86	2	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	77.0797	136	962	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_019117065.1	s__Mediterraneibacter pullicola	76.9256	124	962	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.71	99.71	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:54,215] [INFO] GTDB search result was written to GCF_025567175.1_ASM2556717v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:54,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:54,220] [INFO] DFAST_QC result json was written to GCF_025567175.1_ASM2556717v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:54,220] [INFO] DFAST_QC completed!
[2024-01-24 15:19:54,220] [INFO] Total running time: 0h1m2s