[2023-06-04 22:24:43,432] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:24:43,435] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:24:43,436] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference
[2023-06-04 22:24:45,162] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:24:45,163] [INFO] Task started: Prodigal
[2023-06-04 22:24:45,163] [INFO] Running command: gunzip -c /var/lib/cwl/stga61c9ec2-d097-46f0-a9b5-4939eccb1e1b/GCA_934293875.1_ERR7737955_bin.14_genomic.fna.gz | prodigal -d GCA_934293875.1_ERR7737955_bin.14_genomic.fna/cds.fna -a GCA_934293875.1_ERR7737955_bin.14_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:24:51,287] [INFO] Task succeeded: Prodigal
[2023-06-04 22:24:51,288] [INFO] Task started: HMMsearch
[2023-06-04 22:24:51,288] [INFO] Running command: hmmsearch --tblout GCA_934293875.1_ERR7737955_bin.14_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference/reference_markers.hmm GCA_934293875.1_ERR7737955_bin.14_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:24:51,543] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:24:51,546] [INFO] Found 6/6 markers.
[2023-06-04 22:24:51,571] [INFO] Query marker FASTA was written to GCA_934293875.1_ERR7737955_bin.14_genomic.fna/markers.fasta
[2023-06-04 22:24:51,571] [INFO] Task started: Blastn
[2023-06-04 22:24:51,571] [INFO] Running command: blastn -query GCA_934293875.1_ERR7737955_bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference/reference_markers.fasta -out GCA_934293875.1_ERR7737955_bin.14_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:24:52,206] [INFO] Task succeeded: Blastn
[2023-06-04 22:24:52,210] [INFO] Selected 16 target genomes.
[2023-06-04 22:24:52,211] [INFO] Target genome list was writen to GCA_934293875.1_ERR7737955_bin.14_genomic.fna/target_genomes.txt
[2023-06-04 22:24:52,211] [INFO] Task started: fastANI
[2023-06-04 22:24:52,212] [INFO] Running command: fastANI --query /var/lib/cwl/stga61c9ec2-d097-46f0-a9b5-4939eccb1e1b/GCA_934293875.1_ERR7737955_bin.14_genomic.fna.gz --refList GCA_934293875.1_ERR7737955_bin.14_genomic.fna/target_genomes.txt --output GCA_934293875.1_ERR7737955_bin.14_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:25:00,893] [INFO] Task succeeded: fastANI
[2023-06-04 22:25:00,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:25:00,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:25:00,906] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2023-06-04 22:25:00,906] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 22:25:00,906] [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_000169235.1	39486	39486	suspected-type	True	97.5605	715	847	95	conclusive
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	97.4578	717	847	95	conclusive
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.301	168	847	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.9485	245	847	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.9286	238	847	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.2291	144	847	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.1581	128	847	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.0617	135	847	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.0573	102	847	95	below_threshold
Suipraeoptans intestinalis	strain=68-1-5	GCA_009696485.1	2606628	2606628	type	True	77.7973	65	847	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.6457	121	847	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.2828	87	847	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.0448	85	847	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	76.9402	87	847	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 22:25:00,908] [INFO] DFAST Taxonomy check result was written to GCA_934293875.1_ERR7737955_bin.14_genomic.fna/tc_result.tsv
[2023-06-04 22:25:00,909] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:25:00,909] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:25:00,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference/checkm_data
[2023-06-04 22:25:00,911] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:25:00,946] [INFO] Task started: CheckM
[2023-06-04 22:25:00,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934293875.1_ERR7737955_bin.14_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934293875.1_ERR7737955_bin.14_genomic.fna/checkm_input GCA_934293875.1_ERR7737955_bin.14_genomic.fna/checkm_result
[2023-06-04 22:25:26,516] [INFO] Task succeeded: CheckM
[2023-06-04 22:25:26,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-04 22:25:26,540] [INFO] ===== Completeness check finished =====
[2023-06-04 22:25:26,541] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:25:26,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934293875.1_ERR7737955_bin.14_genomic.fna/markers.fasta)
[2023-06-04 22:25:26,542] [INFO] Task started: Blastn
[2023-06-04 22:25:26,542] [INFO] Running command: blastn -query GCA_934293875.1_ERR7737955_bin.14_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc8a9c0d-263a-41e5-be84-e533b254f95f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934293875.1_ERR7737955_bin.14_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:25:27,595] [INFO] Task succeeded: Blastn
[2023-06-04 22:25:27,600] [INFO] Selected 23 target genomes.
[2023-06-04 22:25:27,600] [INFO] Target genome list was writen to GCA_934293875.1_ERR7737955_bin.14_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:25:27,608] [INFO] Task started: fastANI
[2023-06-04 22:25:27,608] [INFO] Running command: fastANI --query /var/lib/cwl/stga61c9ec2-d097-46f0-a9b5-4939eccb1e1b/GCA_934293875.1_ERR7737955_bin.14_genomic.fna.gz --refList GCA_934293875.1_ERR7737955_bin.14_genomic.fna/target_genomes_gtdb.txt --output GCA_934293875.1_ERR7737955_bin.14_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:25:39,342] [INFO] Task succeeded: fastANI
[2023-06-04 22:25:39,370] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:25:39,370] [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	97.5605	715	847	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_001404875.1	s__Dorea_A longicatena_B	79.5551	257	847	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	-
GCA_000155875.1	s__Bariatricus comes	79.419	163	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_000154065.1	s__Dorea_A longicatena	78.9476	237	847	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_003435815.1	s__CAG-317 sp000433215	78.795	243	847	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	-
GCA_900550865.1	s__Dorea_A sp900550865	78.3857	202	847	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_900543415.1	s__CAG-317 sp900543415	78.1401	141	847	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_000469345.1	s__Eubacterium_I ramulus	78.0921	101	847	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	-
GCA_000433535.1	s__CAG-317 sp000433535	77.8487	154	847	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_016295505.1	s__Dorea_A sp016295505	77.7912	143	847	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_016902415.1	s__Merdimonas massiliensis	77.7004	110	847	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	77.5992	94	847	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_900546495.1	s__Eubacterium_I sp900546495	77.4724	92	847	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	-
GCA_002492335.1	s__UBA7109 sp002492335	77.4548	109	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403455.2	s__Sporofaciens sp000403455	77.3468	107	847	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_910584615.1	s__MD308 sp910584615	77.1303	94	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153925.1	s__Mediterraneibacter torques	76.9402	87	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.42	99.19	0.88	0.82	25	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	76.8686	69	847	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_019113645.1	s__Mediterraneibacter vanvlietii	76.7924	80	847	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	76.564	68	847	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
--------------------------------------------------------------------------------
[2023-06-04 22:25:39,372] [INFO] GTDB search result was written to GCA_934293875.1_ERR7737955_bin.14_genomic.fna/result_gtdb.tsv
[2023-06-04 22:25:39,373] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:25:39,377] [INFO] DFAST_QC result json was written to GCA_934293875.1_ERR7737955_bin.14_genomic.fna/dqc_result.json
[2023-06-04 22:25:39,377] [INFO] DFAST_QC completed!
[2023-06-04 22:25:39,377] [INFO] Total running time: 0h0m56s