[2023-06-18 21:39:28,924] [INFO] DFAST_QC pipeline started.
[2023-06-18 21:39:28,926] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 21:39:28,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference
[2023-06-18 21:39:30,187] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 21:39:30,188] [INFO] Task started: Prodigal
[2023-06-18 21:39:30,188] [INFO] Running command: gunzip -c /var/lib/cwl/stg597d2990-0ecb-4248-8b5d-d70a2b6a3592/GCA_018054585.1_ASM1805458v1_genomic.fna.gz | prodigal -d GCA_018054585.1_ASM1805458v1_genomic.fna/cds.fna -a GCA_018054585.1_ASM1805458v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 21:39:33,904] [INFO] Task succeeded: Prodigal
[2023-06-18 21:39:33,904] [INFO] Task started: HMMsearch
[2023-06-18 21:39:33,904] [INFO] Running command: hmmsearch --tblout GCA_018054585.1_ASM1805458v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference/reference_markers.hmm GCA_018054585.1_ASM1805458v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 21:39:34,119] [INFO] Task succeeded: HMMsearch
[2023-06-18 21:39:34,121] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg597d2990-0ecb-4248-8b5d-d70a2b6a3592/GCA_018054585.1_ASM1805458v1_genomic.fna.gz]
[2023-06-18 21:39:34,143] [INFO] Query marker FASTA was written to GCA_018054585.1_ASM1805458v1_genomic.fna/markers.fasta
[2023-06-18 21:39:34,143] [INFO] Task started: Blastn
[2023-06-18 21:39:34,143] [INFO] Running command: blastn -query GCA_018054585.1_ASM1805458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference/reference_markers.fasta -out GCA_018054585.1_ASM1805458v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:34,750] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:34,756] [INFO] Selected 10 target genomes.
[2023-06-18 21:39:34,756] [INFO] Target genome list was writen to GCA_018054585.1_ASM1805458v1_genomic.fna/target_genomes.txt
[2023-06-18 21:39:34,758] [INFO] Task started: fastANI
[2023-06-18 21:39:34,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg597d2990-0ecb-4248-8b5d-d70a2b6a3592/GCA_018054585.1_ASM1805458v1_genomic.fna.gz --refList GCA_018054585.1_ASM1805458v1_genomic.fna/target_genomes.txt --output GCA_018054585.1_ASM1805458v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 21:39:40,287] [INFO] Task succeeded: fastANI
[2023-06-18 21:39:40,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 21:39:40,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 21:39:40,296] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 21:39:40,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 21:39:40,297] [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
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	78.9571	111	357	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	78.8805	112	357	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	78.7176	164	357	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.7119	166	357	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	78.4903	110	357	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.2069	79	357	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.0128	98	357	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.1544	87	357	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 21:39:40,300] [INFO] DFAST Taxonomy check result was written to GCA_018054585.1_ASM1805458v1_genomic.fna/tc_result.tsv
[2023-06-18 21:39:40,303] [INFO] ===== Taxonomy check completed =====
[2023-06-18 21:39:40,303] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 21:39:40,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference/checkm_data
[2023-06-18 21:39:40,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 21:39:40,327] [INFO] Task started: CheckM
[2023-06-18 21:39:40,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054585.1_ASM1805458v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054585.1_ASM1805458v1_genomic.fna/checkm_input GCA_018054585.1_ASM1805458v1_genomic.fna/checkm_result
[2023-06-18 21:39:58,620] [INFO] Task succeeded: CheckM
[2023-06-18 21:39:58,622] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 21:39:58,666] [INFO] ===== Completeness check finished =====
[2023-06-18 21:39:58,666] [INFO] ===== Start GTDB Search =====
[2023-06-18 21:39:58,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054585.1_ASM1805458v1_genomic.fna/markers.fasta)
[2023-06-18 21:39:58,667] [INFO] Task started: Blastn
[2023-06-18 21:39:58,668] [INFO] Running command: blastn -query GCA_018054585.1_ASM1805458v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9231dea5-3a60-41e5-b690-732bc40a0461/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054585.1_ASM1805458v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 21:39:59,503] [INFO] Task succeeded: Blastn
[2023-06-18 21:39:59,507] [INFO] Selected 13 target genomes.
[2023-06-18 21:39:59,508] [INFO] Target genome list was writen to GCA_018054585.1_ASM1805458v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 21:39:59,510] [INFO] Task started: fastANI
[2023-06-18 21:39:59,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg597d2990-0ecb-4248-8b5d-d70a2b6a3592/GCA_018054585.1_ASM1805458v1_genomic.fna.gz --refList GCA_018054585.1_ASM1805458v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054585.1_ASM1805458v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 21:40:05,350] [INFO] Task succeeded: fastANI
[2023-06-18 21:40:05,364] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 21:40:05,365] [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_003324125.1	s__Gemmiger qucibialis	99.4132	351	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.44	97.30	0.87	0.66	39	conclusive
GCA_004561545.1	s__Gemmiger sp004561545	80.3365	169	357	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	80.1166	200	357	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_900772715.1	s__Gemmiger sp900772715	79.9127	97	357	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_004554775.1	s__Gemmiger variabilis_B	79.8148	230	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.40	97.89	0.89	0.88	3	-
GCA_905214345.1	s__Gemmiger sp905214345	79.658	201	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900095.1	s__Gemmiger formicilis_A	79.6335	200	357	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_019114415.1	s__Gemmiger faecavium	79.3387	169	357	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_900545545.1	s__Gemmiger sp900545545	79.1707	183	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	96.26	96.20	0.77	0.76	3	-
GCF_014982805.1	s__Gemmiger sp014982805	79.1409	170	357	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_019116445.1	s__Gemmiger excrementigallinarum	78.7619	165	357	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_003343905.1	s__Gemmiger variabilis_C	78.7271	184	357	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_019116485.1	s__Gemmiger excrementavium	78.6772	170	357	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 21:40:05,370] [INFO] GTDB search result was written to GCA_018054585.1_ASM1805458v1_genomic.fna/result_gtdb.tsv
[2023-06-18 21:40:05,370] [INFO] ===== GTDB Search completed =====
[2023-06-18 21:40:05,378] [INFO] DFAST_QC result json was written to GCA_018054585.1_ASM1805458v1_genomic.fna/dqc_result.json
[2023-06-18 21:40:05,378] [INFO] DFAST_QC completed!
[2023-06-18 21:40:05,378] [INFO] Total running time: 0h0m36s