[2023-06-28 19:48:51,090] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:48:51,098] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:48:51,098] [INFO] DQC Reference Directory: /var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference
[2023-06-28 19:48:52,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:48:52,502] [INFO] Task started: Prodigal
[2023-06-28 19:48:52,502] [INFO] Running command: gunzip -c /var/lib/cwl/stgec3f434e-8ede-4128-947a-52bfcea8837e/GCA_944382795.1_E16_bin44_genomic.fna.gz | prodigal -d GCA_944382795.1_E16_bin44_genomic.fna/cds.fna -a GCA_944382795.1_E16_bin44_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:48:58,185] [INFO] Task succeeded: Prodigal
[2023-06-28 19:48:58,186] [INFO] Task started: HMMsearch
[2023-06-28 19:48:58,186] [INFO] Running command: hmmsearch --tblout GCA_944382795.1_E16_bin44_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference/reference_markers.hmm GCA_944382795.1_E16_bin44_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:48:58,414] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:48:58,416] [INFO] Found 6/6 markers.
[2023-06-28 19:48:58,440] [INFO] Query marker FASTA was written to GCA_944382795.1_E16_bin44_genomic.fna/markers.fasta
[2023-06-28 19:48:58,440] [INFO] Task started: Blastn
[2023-06-28 19:48:58,441] [INFO] Running command: blastn -query GCA_944382795.1_E16_bin44_genomic.fna/markers.fasta -db /var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference/reference_markers.fasta -out GCA_944382795.1_E16_bin44_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:48:59,081] [INFO] Task succeeded: Blastn
[2023-06-28 19:48:59,086] [INFO] Selected 22 target genomes.
[2023-06-28 19:48:59,087] [INFO] Target genome list was writen to GCA_944382795.1_E16_bin44_genomic.fna/target_genomes.txt
[2023-06-28 19:48:59,094] [INFO] Task started: fastANI
[2023-06-28 19:48:59,094] [INFO] Running command: fastANI --query /var/lib/cwl/stgec3f434e-8ede-4128-947a-52bfcea8837e/GCA_944382795.1_E16_bin44_genomic.fna.gz --refList GCA_944382795.1_E16_bin44_genomic.fna/target_genomes.txt --output GCA_944382795.1_E16_bin44_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:49:09,395] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:09,396] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:49:09,397] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:49:09,409] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 19:49:09,410] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 19:49:09,410] [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
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.9848	199	586	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	76.9878	68	586	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	76.9866	57	586	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	76.9856	69	586	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	76.6321	70	586	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	76.6321	70	586	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.5453	66	586	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.5409	58	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 19:49:09,411] [INFO] DFAST Taxonomy check result was written to GCA_944382795.1_E16_bin44_genomic.fna/tc_result.tsv
[2023-06-28 19:49:09,412] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:49:09,412] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:49:09,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference/checkm_data
[2023-06-28 19:49:09,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:49:09,435] [INFO] Task started: CheckM
[2023-06-28 19:49:09,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944382795.1_E16_bin44_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944382795.1_E16_bin44_genomic.fna/checkm_input GCA_944382795.1_E16_bin44_genomic.fna/checkm_result
[2023-06-28 19:49:32,509] [INFO] Task succeeded: CheckM
[2023-06-28 19:49:32,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.92%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 19:49:32,532] [INFO] ===== Completeness check finished =====
[2023-06-28 19:49:32,532] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:49:32,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944382795.1_E16_bin44_genomic.fna/markers.fasta)
[2023-06-28 19:49:32,533] [INFO] Task started: Blastn
[2023-06-28 19:49:32,533] [INFO] Running command: blastn -query GCA_944382795.1_E16_bin44_genomic.fna/markers.fasta -db /var/lib/cwl/stgd468ea18-c5ac-4b84-a01e-79dc0d655ab6/dqc_reference/reference_markers_gtdb.fasta -out GCA_944382795.1_E16_bin44_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:49:33,598] [INFO] Task succeeded: Blastn
[2023-06-28 19:49:33,603] [INFO] Selected 17 target genomes.
[2023-06-28 19:49:33,603] [INFO] Target genome list was writen to GCA_944382795.1_E16_bin44_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:49:33,609] [INFO] Task started: fastANI
[2023-06-28 19:49:33,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgec3f434e-8ede-4128-947a-52bfcea8837e/GCA_944382795.1_E16_bin44_genomic.fna.gz --refList GCA_944382795.1_E16_bin44_genomic.fna/target_genomes_gtdb.txt --output GCA_944382795.1_E16_bin44_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:49:41,186] [INFO] Task succeeded: fastANI
[2023-06-28 19:49:41,205] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:49:41,205] [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
GCA_018883715.1	s__Fournierella pullistercoris	99.1212	465	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002161595.1	s__Fournierella sp002161595	79.1628	217	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.81	98.81	0.92	0.92	2	-
GCF_004345265.1	s__Fournierella massiliensis	78.9964	198	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.99	99.99	1.00	1.00	3	-
GCF_002160145.1	s__Fournierella sp002160145	78.9568	211	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	98.11	98.11	0.91	0.91	2	-
GCF_002159185.1	s__Fournierella sp002159185	78.892	197	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160955.1	s__Gemmiger_A avium	77.9715	114	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger_A	95.0	98.36	98.15	0.86	0.80	3	-
GCA_004555865.1	s__SFJ001 sp004555865	77.7242	88	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__SFJ001	95.0	98.44	98.34	0.90	0.89	3	-
GCA_019118765.1	s__Fournierella merdavium	77.6651	112	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116345.1	s__Fournierella merdipullorum	77.6604	115	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558145.1	s__Fournierella excrementavium	77.5891	130	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	97.60	97.45	0.91	0.87	5	-
GCA_900543285.1	s__Fournierella sp900543285	77.391	103	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	99.38	98.75	0.91	0.84	3	-
GCA_004558805.1	s__Faecalibacterium prausnitzii_M	77.1219	65	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.98	97.83	0.94	0.93	3	-
GCF_003324125.1	s__Gemmiger qucibialis	76.8208	57	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.44	97.30	0.87	0.66	39	-
GCF_014982805.1	s__Gemmiger sp014982805	76.6192	76	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539695.1	s__Gemmiger sp900539695	76.5509	53	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.42	97.91	0.86	0.79	8	-
GCA_904374465.1	s__Gemmiger sp904374465	76.4744	80	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540595.1	s__Gemmiger sp900540595	76.3313	53	586	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.09	95.97	0.86	0.82	4	-
--------------------------------------------------------------------------------
[2023-06-28 19:49:41,208] [INFO] GTDB search result was written to GCA_944382795.1_E16_bin44_genomic.fna/result_gtdb.tsv
[2023-06-28 19:49:41,208] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:49:41,214] [INFO] DFAST_QC result json was written to GCA_944382795.1_E16_bin44_genomic.fna/dqc_result.json
[2023-06-28 19:49:41,215] [INFO] DFAST_QC completed!
[2023-06-28 19:49:41,215] [INFO] Total running time: 0h0m50s