[2023-06-13 16:47:20,027] [INFO] DFAST_QC pipeline started.
[2023-06-13 16:47:20,030] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 16:47:20,030] [INFO] DQC Reference Directory: /var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference
[2023-06-13 16:47:21,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 16:47:21,240] [INFO] Task started: Prodigal
[2023-06-13 16:47:21,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c4f78e5-8bfc-486f-81fe-cccf19487eee/GCA_928721735.1_min17_bin23_genomic.fna.gz | prodigal -d GCA_928721735.1_min17_bin23_genomic.fna/cds.fna -a GCA_928721735.1_min17_bin23_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 16:47:27,791] [INFO] Task succeeded: Prodigal
[2023-06-13 16:47:27,792] [INFO] Task started: HMMsearch
[2023-06-13 16:47:27,792] [INFO] Running command: hmmsearch --tblout GCA_928721735.1_min17_bin23_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference/reference_markers.hmm GCA_928721735.1_min17_bin23_genomic.fna/protein.faa > /dev/null
[2023-06-13 16:47:28,024] [INFO] Task succeeded: HMMsearch
[2023-06-13 16:47:28,025] [INFO] Found 6/6 markers.
[2023-06-13 16:47:28,046] [INFO] Query marker FASTA was written to GCA_928721735.1_min17_bin23_genomic.fna/markers.fasta
[2023-06-13 16:47:28,047] [INFO] Task started: Blastn
[2023-06-13 16:47:28,047] [INFO] Running command: blastn -query GCA_928721735.1_min17_bin23_genomic.fna/markers.fasta -db /var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference/reference_markers.fasta -out GCA_928721735.1_min17_bin23_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:47:28,738] [INFO] Task succeeded: Blastn
[2023-06-13 16:47:28,743] [INFO] Selected 24 target genomes.
[2023-06-13 16:47:28,744] [INFO] Target genome list was writen to GCA_928721735.1_min17_bin23_genomic.fna/target_genomes.txt
[2023-06-13 16:47:28,748] [INFO] Task started: fastANI
[2023-06-13 16:47:28,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c4f78e5-8bfc-486f-81fe-cccf19487eee/GCA_928721735.1_min17_bin23_genomic.fna.gz --refList GCA_928721735.1_min17_bin23_genomic.fna/target_genomes.txt --output GCA_928721735.1_min17_bin23_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 16:47:41,295] [INFO] Task succeeded: fastANI
[2023-06-13 16:47:41,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 16:47:41,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 16:47:41,321] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 16:47:41,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 16:47:41,322] [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
Thermophilibacter mediterraneus	strain=Marseille-P3256	GCA_900119385.1	1871031	1871031	type	True	77.6761	76	644	95	below_threshold
Collinsella vaginalis	strain=Marseille-P2666	GCA_900176655.1	1870987	1870987	type	True	77.3012	64	644	95	below_threshold
Parolsenella massiliensis	strain=Marseille-P3237	GCA_900143685.1	1871022	1871022	type	True	77.2919	78	644	95	below_threshold
Berryella intestinalis	strain=68-1-3	GCA_000814825.1	1531429	1531429	type	True	77.2459	59	644	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	77.1922	73	644	95	below_threshold
Raoultibacter timonensis	strain=Marseille-P3277	GCA_900240215.1	1907662	1907662	type	True	77.1668	78	644	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	77.1266	114	644	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_000422625.1	580026	580026	type	True	77.114	78	644	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	77.1135	92	644	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	77.0624	93	644	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	77.0605	91	644	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	77.0397	96	644	95	below_threshold
Thermophilibacter provencensis	strain=Marseille-P2912	GCA_900128445.1	1852386	1852386	type	True	77.0249	83	644	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	76.8839	90	644	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	76.8637	80	644	95	below_threshold
Slackia equolifaciens	strain=DSM 24851	GCA_003725995.1	498718	498718	type	True	76.8237	55	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 16:47:41,324] [INFO] DFAST Taxonomy check result was written to GCA_928721735.1_min17_bin23_genomic.fna/tc_result.tsv
[2023-06-13 16:47:41,325] [INFO] ===== Taxonomy check completed =====
[2023-06-13 16:47:41,325] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 16:47:41,325] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference/checkm_data
[2023-06-13 16:47:41,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 16:47:41,352] [INFO] Task started: CheckM
[2023-06-13 16:47:41,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_928721735.1_min17_bin23_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_928721735.1_min17_bin23_genomic.fna/checkm_input GCA_928721735.1_min17_bin23_genomic.fna/checkm_result
[2023-06-13 16:48:05,932] [INFO] Task succeeded: CheckM
[2023-06-13 16:48:05,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 16:48:05,955] [INFO] ===== Completeness check finished =====
[2023-06-13 16:48:05,955] [INFO] ===== Start GTDB Search =====
[2023-06-13 16:48:05,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_928721735.1_min17_bin23_genomic.fna/markers.fasta)
[2023-06-13 16:48:05,956] [INFO] Task started: Blastn
[2023-06-13 16:48:05,956] [INFO] Running command: blastn -query GCA_928721735.1_min17_bin23_genomic.fna/markers.fasta -db /var/lib/cwl/stgf968611a-da78-4ba3-9258-f5010e239219/dqc_reference/reference_markers_gtdb.fasta -out GCA_928721735.1_min17_bin23_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 16:48:07,030] [INFO] Task succeeded: Blastn
[2023-06-13 16:48:07,035] [INFO] Selected 14 target genomes.
[2023-06-13 16:48:07,035] [INFO] Target genome list was writen to GCA_928721735.1_min17_bin23_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 16:48:07,040] [INFO] Task started: fastANI
[2023-06-13 16:48:07,040] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c4f78e5-8bfc-486f-81fe-cccf19487eee/GCA_928721735.1_min17_bin23_genomic.fna.gz --refList GCA_928721735.1_min17_bin23_genomic.fna/target_genomes_gtdb.txt --output GCA_928721735.1_min17_bin23_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 16:48:12,837] [INFO] Task succeeded: fastANI
[2023-06-13 16:48:12,853] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 16:48:12,853] [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_900544245.1	s__QAMH01 sp900544245	97.1006	462	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	97.45	97.43	0.84	0.81	3	conclusive
GCA_003149935.1	s__QAMH01 sp003149935	86.079	478	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	96.22	96.22	0.86	0.86	2	-
GCA_900756605.1	s__QAMH01 sp900756605	85.9299	281	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	97.24	97.24	0.74	0.74	2	-
GCA_900556425.1	s__QAMH01 sp900556425	85.6724	252	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783175.1	s__CACZQA01 sp902783175	78.5941	139	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__CACZQA01	95.0	97.45	97.17	0.71	0.71	3	-
GCA_900758075.1	s__CACZQA01 sp900758075	78.5891	122	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__CACZQA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783925.1	s__QAMH01 sp902783925	78.1671	132	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__QAMH01;g__QAMH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779675.1	s__UBA1367 sp902779675	77.1283	75	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	97.95	97.30	0.86	0.82	4	-
GCF_003416765.1	s__Paratractidigestivibacter faecalis	76.7972	71	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Paratractidigestivibacter	95.0	96.79	95.48	0.89	0.83	10	-
GCA_900751755.1	s__Collinsella sp900751755	76.7163	52	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.91	99.91	0.92	0.92	2	-
GCA_902778135.1	s__UBA1367 sp902778135	76.7046	67	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__UBA1367	95.0	98.30	98.30	0.89	0.89	2	-
GCA_900544205.1	s__Collinsella sp900544205	76.5257	56	644	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-13 16:48:12,855] [INFO] GTDB search result was written to GCA_928721735.1_min17_bin23_genomic.fna/result_gtdb.tsv
[2023-06-13 16:48:12,856] [INFO] ===== GTDB Search completed =====
[2023-06-13 16:48:12,862] [INFO] DFAST_QC result json was written to GCA_928721735.1_min17_bin23_genomic.fna/dqc_result.json
[2023-06-13 16:48:12,862] [INFO] DFAST_QC completed!
[2023-06-13 16:48:12,862] [INFO] Total running time: 0h0m53s