[2023-06-28 06:09:52,425] [INFO] DFAST_QC pipeline started.
[2023-06-28 06:09:52,427] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 06:09:52,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference
[2023-06-28 06:09:53,628] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 06:09:53,629] [INFO] Task started: Prodigal
[2023-06-28 06:09:53,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg3c593524-a7c5-4735-aabf-3d6cd06508c7/GCA_944387985.1_BRZ_PF_bin41_genomic.fna.gz | prodigal -d GCA_944387985.1_BRZ_PF_bin41_genomic.fna/cds.fna -a GCA_944387985.1_BRZ_PF_bin41_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 06:10:01,081] [INFO] Task succeeded: Prodigal
[2023-06-28 06:10:01,082] [INFO] Task started: HMMsearch
[2023-06-28 06:10:01,082] [INFO] Running command: hmmsearch --tblout GCA_944387985.1_BRZ_PF_bin41_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference/reference_markers.hmm GCA_944387985.1_BRZ_PF_bin41_genomic.fna/protein.faa > /dev/null
[2023-06-28 06:10:01,284] [INFO] Task succeeded: HMMsearch
[2023-06-28 06:10:01,286] [INFO] Found 6/6 markers.
[2023-06-28 06:10:01,311] [INFO] Query marker FASTA was written to GCA_944387985.1_BRZ_PF_bin41_genomic.fna/markers.fasta
[2023-06-28 06:10:01,312] [INFO] Task started: Blastn
[2023-06-28 06:10:01,312] [INFO] Running command: blastn -query GCA_944387985.1_BRZ_PF_bin41_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference/reference_markers.fasta -out GCA_944387985.1_BRZ_PF_bin41_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:10:02,045] [INFO] Task succeeded: Blastn
[2023-06-28 06:10:02,048] [INFO] Selected 9 target genomes.
[2023-06-28 06:10:02,048] [INFO] Target genome list was writen to GCA_944387985.1_BRZ_PF_bin41_genomic.fna/target_genomes.txt
[2023-06-28 06:10:02,049] [INFO] Task started: fastANI
[2023-06-28 06:10:02,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c593524-a7c5-4735-aabf-3d6cd06508c7/GCA_944387985.1_BRZ_PF_bin41_genomic.fna.gz --refList GCA_944387985.1_BRZ_PF_bin41_genomic.fna/target_genomes.txt --output GCA_944387985.1_BRZ_PF_bin41_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 06:10:06,548] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:06,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 06:10:06,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 06:10:06,556] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 06:10:06,556] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 06:10:06,556] [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 gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	83.4518	504	865	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	81.326	420	865	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	80.9301	428	865	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	80.8188	431	865	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	80.6238	429	865	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.2358	242	865	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3629	146	865	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 06:10:06,558] [INFO] DFAST Taxonomy check result was written to GCA_944387985.1_BRZ_PF_bin41_genomic.fna/tc_result.tsv
[2023-06-28 06:10:06,560] [INFO] ===== Taxonomy check completed =====
[2023-06-28 06:10:06,560] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 06:10:06,560] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference/checkm_data
[2023-06-28 06:10:06,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 06:10:06,606] [INFO] Task started: CheckM
[2023-06-28 06:10:06,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944387985.1_BRZ_PF_bin41_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944387985.1_BRZ_PF_bin41_genomic.fna/checkm_input GCA_944387985.1_BRZ_PF_bin41_genomic.fna/checkm_result
[2023-06-28 06:10:32,303] [INFO] Task succeeded: CheckM
[2023-06-28 06:10:32,304] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 06:10:32,331] [INFO] ===== Completeness check finished =====
[2023-06-28 06:10:32,331] [INFO] ===== Start GTDB Search =====
[2023-06-28 06:10:32,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944387985.1_BRZ_PF_bin41_genomic.fna/markers.fasta)
[2023-06-28 06:10:32,332] [INFO] Task started: Blastn
[2023-06-28 06:10:32,332] [INFO] Running command: blastn -query GCA_944387985.1_BRZ_PF_bin41_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b07e892-570e-41b0-9352-82e31f344cc7/dqc_reference/reference_markers_gtdb.fasta -out GCA_944387985.1_BRZ_PF_bin41_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 06:10:33,626] [INFO] Task succeeded: Blastn
[2023-06-28 06:10:33,630] [INFO] Selected 7 target genomes.
[2023-06-28 06:10:33,630] [INFO] Target genome list was writen to GCA_944387985.1_BRZ_PF_bin41_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 06:10:33,635] [INFO] Task started: fastANI
[2023-06-28 06:10:33,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg3c593524-a7c5-4735-aabf-3d6cd06508c7/GCA_944387985.1_BRZ_PF_bin41_genomic.fna.gz --refList GCA_944387985.1_BRZ_PF_bin41_genomic.fna/target_genomes_gtdb.txt --output GCA_944387985.1_BRZ_PF_bin41_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 06:10:38,884] [INFO] Task succeeded: fastANI
[2023-06-28 06:10:38,891] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 06:10:38,892] [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_019116585.1	s__Faecalibacterium gallistercoris	98.1232	659	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.23	98.17	0.89	0.87	6	conclusive
GCA_019119685.1	s__Faecalibacterium faecigallinarum	91.8942	570	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.44	97.44	0.75	0.75	2	-
GCA_019113345.1	s__Faecalibacterium intestinigallinarum	90.0622	566	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.07	98.05	0.85	0.83	3	-
GCA_019118985.1	s__Faecalibacterium faecipullorum	87.602	478	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160915.1	s__Faecalibacterium avium	87.4336	629	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.16	97.86	0.90	0.86	4	-
GCF_002160895.1	s__Faecalibacterium sp002160895	86.5291	624	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.38	97.36	0.82	0.81	3	-
GCA_904394215.1	s__Faecalibacterium sp904394215	85.4261	520	865	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 06:10:38,894] [INFO] GTDB search result was written to GCA_944387985.1_BRZ_PF_bin41_genomic.fna/result_gtdb.tsv
[2023-06-28 06:10:38,894] [INFO] ===== GTDB Search completed =====
[2023-06-28 06:10:38,897] [INFO] DFAST_QC result json was written to GCA_944387985.1_BRZ_PF_bin41_genomic.fna/dqc_result.json
[2023-06-28 06:10:38,897] [INFO] DFAST_QC completed!
[2023-06-28 06:10:38,897] [INFO] Total running time: 0h0m46s