[2023-06-04 18:59:13,593] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:59:13,596] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:59:13,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference
[2023-06-04 18:59:14,783] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:59:14,784] [INFO] Task started: Prodigal
[2023-06-04 18:59:14,785] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2f6f89c-7d7c-4c41-a331-746af6c8cb0d/GCA_934855995.1_MTG234_bin.40.fa_genomic.fna.gz | prodigal -d GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/cds.fna -a GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:59:24,094] [INFO] Task succeeded: Prodigal
[2023-06-04 18:59:24,094] [INFO] Task started: HMMsearch
[2023-06-04 18:59:24,094] [INFO] Running command: hmmsearch --tblout GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference/reference_markers.hmm GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:59:24,367] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:59:24,368] [INFO] Found 6/6 markers.
[2023-06-04 18:59:24,402] [INFO] Query marker FASTA was written to GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/markers.fasta
[2023-06-04 18:59:24,403] [INFO] Task started: Blastn
[2023-06-04 18:59:24,403] [INFO] Running command: blastn -query GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference/reference_markers.fasta -out GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:59:25,145] [INFO] Task succeeded: Blastn
[2023-06-04 18:59:25,150] [INFO] Selected 11 target genomes.
[2023-06-04 18:59:25,150] [INFO] Target genome list was writen to GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/target_genomes.txt
[2023-06-04 18:59:25,152] [INFO] Task started: fastANI
[2023-06-04 18:59:25,153] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2f6f89c-7d7c-4c41-a331-746af6c8cb0d/GCA_934855995.1_MTG234_bin.40.fa_genomic.fna.gz --refList GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/target_genomes.txt --output GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:59:30,064] [INFO] Task succeeded: fastANI
[2023-06-04 18:59:30,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:59:30,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:59:30,072] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:59:30,072] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:59:30,073] [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
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	80.6593	382	1034	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	80.5645	392	1034	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	79.2122	255	1034	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	79.0817	246	1034	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	79.0407	243	1034	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.4486	177	1034	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	77.8279	185	1034	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:59:30,081] [INFO] DFAST Taxonomy check result was written to GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/tc_result.tsv
[2023-06-04 18:59:30,082] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:59:30,082] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:59:30,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference/checkm_data
[2023-06-04 18:59:30,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:59:30,124] [INFO] Task started: CheckM
[2023-06-04 18:59:30,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/checkm_input GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/checkm_result
[2023-06-04 19:00:02,086] [INFO] Task succeeded: CheckM
[2023-06-04 19:00:02,087] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 19:00:02,114] [INFO] ===== Completeness check finished =====
[2023-06-04 19:00:02,115] [INFO] ===== Start GTDB Search =====
[2023-06-04 19:00:02,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/markers.fasta)
[2023-06-04 19:00:02,116] [INFO] Task started: Blastn
[2023-06-04 19:00:02,116] [INFO] Running command: blastn -query GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg76fc8b53-0c66-4c9e-8265-f8b15bd1f5cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 19:00:03,411] [INFO] Task succeeded: Blastn
[2023-06-04 19:00:03,417] [INFO] Selected 8 target genomes.
[2023-06-04 19:00:03,417] [INFO] Target genome list was writen to GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 19:00:03,420] [INFO] Task started: fastANI
[2023-06-04 19:00:03,421] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2f6f89c-7d7c-4c41-a331-746af6c8cb0d/GCA_934855995.1_MTG234_bin.40.fa_genomic.fna.gz --refList GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 19:00:09,960] [INFO] Task succeeded: fastANI
[2023-06-04 19:00:09,972] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 19:00:09,972] [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_900167555.1	s__Gemmiger formicilis	97.2758	808	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.67	96.73	0.89	0.78	43	conclusive
GCF_018784445.1	s__Gemmiger sp900540775	88.2075	753	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.04	97.97	0.87	0.81	8	-
GCA_900540595.1	s__Gemmiger sp900540595	87.3844	654	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.09	95.97	0.86	0.82	4	-
GCA_900554145.1	s__Gemmiger sp900554145	85.7721	498	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	98.15	98.15	0.80	0.80	2	-
GCA_004554775.1	s__Gemmiger variabilis_B	83.6235	585	1034	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_900539695.1	s__Gemmiger sp900539695	83.5388	526	1034	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_004552305.1	s__Gemmiger variabilis_A	81.9281	425	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	97.82	96.59	0.82	0.70	4	-
GCA_003343905.1	s__Gemmiger variabilis_C	80.8406	411	1034	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 19:00:09,975] [INFO] GTDB search result was written to GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/result_gtdb.tsv
[2023-06-04 19:00:09,975] [INFO] ===== GTDB Search completed =====
[2023-06-04 19:00:09,978] [INFO] DFAST_QC result json was written to GCA_934855995.1_MTG234_bin.40.fa_genomic.fna/dqc_result.json
[2023-06-04 19:00:09,979] [INFO] DFAST_QC completed!
[2023-06-04 19:00:09,979] [INFO] Total running time: 0h0m56s