[2023-06-29 23:31:59,579] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:31:59,582] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:31:59,582] [INFO] DQC Reference Directory: /var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference
[2023-06-29 23:32:00,868] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:32:00,869] [INFO] Task started: Prodigal
[2023-06-29 23:32:00,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f26f0d3-bf30-4e75-942f-34b67ddaf0de/GCA_900765005.1_SRS259531_2_genomic.fna.gz | prodigal -d GCA_900765005.1_SRS259531_2_genomic.fna/cds.fna -a GCA_900765005.1_SRS259531_2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:32:07,868] [INFO] Task succeeded: Prodigal
[2023-06-29 23:32:07,869] [INFO] Task started: HMMsearch
[2023-06-29 23:32:07,869] [INFO] Running command: hmmsearch --tblout GCA_900765005.1_SRS259531_2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference/reference_markers.hmm GCA_900765005.1_SRS259531_2_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:32:08,186] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:32:08,188] [INFO] Found 6/6 markers.
[2023-06-29 23:32:08,226] [INFO] Query marker FASTA was written to GCA_900765005.1_SRS259531_2_genomic.fna/markers.fasta
[2023-06-29 23:32:08,227] [INFO] Task started: Blastn
[2023-06-29 23:32:08,227] [INFO] Running command: blastn -query GCA_900765005.1_SRS259531_2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference/reference_markers.fasta -out GCA_900765005.1_SRS259531_2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:32:08,925] [INFO] Task succeeded: Blastn
[2023-06-29 23:32:08,929] [INFO] Selected 33 target genomes.
[2023-06-29 23:32:08,929] [INFO] Target genome list was writen to GCA_900765005.1_SRS259531_2_genomic.fna/target_genomes.txt
[2023-06-29 23:32:08,932] [INFO] Task started: fastANI
[2023-06-29 23:32:08,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f26f0d3-bf30-4e75-942f-34b67ddaf0de/GCA_900765005.1_SRS259531_2_genomic.fna.gz --refList GCA_900765005.1_SRS259531_2_genomic.fna/target_genomes.txt --output GCA_900765005.1_SRS259531_2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:32:30,520] [INFO] Task succeeded: fastANI
[2023-06-29 23:32:30,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:32:30,521] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:32:30,534] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:32:30,534] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:32:30,534] [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
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.8845	80	939	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.6123	102	939	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.9084	71	939	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.852	72	939	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.6971	75	939	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.563	79	939	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.5598	78	939	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	76.5532	60	939	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.4325	58	939	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	76.1971	67	939	95	below_threshold
Enterocloster clostridioformis	strain=FDAARGOS_1529	GCA_020297485.1	1531	1531	suspected-type	True	76.1548	54	939	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	76.1399	53	939	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	75.991	50	939	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	75.9689	54	939	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	75.8489	52	939	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:32:30,536] [INFO] DFAST Taxonomy check result was written to GCA_900765005.1_SRS259531_2_genomic.fna/tc_result.tsv
[2023-06-29 23:32:30,537] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:32:30,538] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:32:30,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference/checkm_data
[2023-06-29 23:32:30,540] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:32:30,575] [INFO] Task started: CheckM
[2023-06-29 23:32:30,576] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900765005.1_SRS259531_2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900765005.1_SRS259531_2_genomic.fna/checkm_input GCA_900765005.1_SRS259531_2_genomic.fna/checkm_result
[2023-06-29 23:32:58,129] [INFO] Task succeeded: CheckM
[2023-06-29 23:32:58,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:32:58,156] [INFO] ===== Completeness check finished =====
[2023-06-29 23:32:58,156] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:32:58,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900765005.1_SRS259531_2_genomic.fna/markers.fasta)
[2023-06-29 23:32:58,157] [INFO] Task started: Blastn
[2023-06-29 23:32:58,157] [INFO] Running command: blastn -query GCA_900765005.1_SRS259531_2_genomic.fna/markers.fasta -db /var/lib/cwl/stg4161e169-69a4-4161-abf4-78ffa3780834/dqc_reference/reference_markers_gtdb.fasta -out GCA_900765005.1_SRS259531_2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:32:59,294] [INFO] Task succeeded: Blastn
[2023-06-29 23:32:59,298] [INFO] Selected 20 target genomes.
[2023-06-29 23:32:59,298] [INFO] Target genome list was writen to GCA_900765005.1_SRS259531_2_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:32:59,306] [INFO] Task started: fastANI
[2023-06-29 23:32:59,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f26f0d3-bf30-4e75-942f-34b67ddaf0de/GCA_900765005.1_SRS259531_2_genomic.fna.gz --refList GCA_900765005.1_SRS259531_2_genomic.fna/target_genomes_gtdb.txt --output GCA_900765005.1_SRS259531_2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:33:11,944] [INFO] Task succeeded: fastANI
[2023-06-29 23:33:11,970] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:33:11,970] [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_018223435.1	s__Limivivens sp900543575	97.902	846	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	conclusive
GCF_003463065.1	s__Limivivens sp900066135	86.4555	670	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.47	97.63	0.91	0.79	5	-
GCA_900551235.1	s__UMGS1375 sp900551235	79.0482	75	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363135.1	s__Choladousia sp902363135	77.8741	88	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	98.66	98.47	0.96	0.95	4	-
GCA_905214955.1	s__Limivivens sp905214955	77.8353	144	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713105.1	s__Limivivens merdigallinarum	77.7478	136	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.32	98.32	0.87	0.87	2	-
GCA_902362725.1	s__Merdisoma sp900066385	77.5366	118	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	98.97	97.93	0.91	0.83	3	-
GCA_002361955.1	s__CAG-56 sp002361955	77.1873	97	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.90	99.85	0.92	0.90	5	-
GCA_900752065.1	s__CAG-56 sp900752065	77.0055	83	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900553635.1	s__Merdisoma sp900553635	76.8072	78	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdisoma	95.0	97.48	97.13	0.82	0.78	3	-
GCA_004793585.1	s__CAG-56 sp004793585	76.5935	62	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	98.07	97.91	0.77	0.75	12	-
GCA_900544685.1	s__Marvinbryantia sp900544685	76.5442	67	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160985.1	s__Lachnoclostridium_B stercoravium	76.3228	65	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	98.37	98.26	0.93	0.92	3	-
GCA_019112735.1	s__Mediterraneibacter guildfordensis	76.3089	68	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016901695.1	s__Lachnoclostridium_B massiliensis_A	76.109	57	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003885045.1	s__Schaedlerella arabinosiphila	75.9063	65	939	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.52	96.80	0.74	0.68	10	-
--------------------------------------------------------------------------------
[2023-06-29 23:33:11,973] [INFO] GTDB search result was written to GCA_900765005.1_SRS259531_2_genomic.fna/result_gtdb.tsv
[2023-06-29 23:33:11,973] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:33:11,978] [INFO] DFAST_QC result json was written to GCA_900765005.1_SRS259531_2_genomic.fna/dqc_result.json
[2023-06-29 23:33:11,978] [INFO] DFAST_QC completed!
[2023-06-29 23:33:11,978] [INFO] Total running time: 0h1m12s