[2023-06-16 19:10:44,624] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:10:44,626] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:10:44,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference
[2023-06-16 19:10:45,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:10:45,842] [INFO] Task started: Prodigal
[2023-06-16 19:10:45,843] [INFO] Running command: gunzip -c /var/lib/cwl/stgc111b407-a882-44ff-b9b6-0c03cbe8a9fb/GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna.gz | prodigal -d GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/cds.fna -a GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:10:51,883] [INFO] Task succeeded: Prodigal
[2023-06-16 19:10:51,883] [INFO] Task started: HMMsearch
[2023-06-16 19:10:51,883] [INFO] Running command: hmmsearch --tblout GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference/reference_markers.hmm GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:10:52,051] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:10:52,052] [INFO] Found 6/6 markers.
[2023-06-16 19:10:52,075] [INFO] Query marker FASTA was written to GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/markers.fasta
[2023-06-16 19:10:52,076] [INFO] Task started: Blastn
[2023-06-16 19:10:52,076] [INFO] Running command: blastn -query GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference/reference_markers.fasta -out GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:10:52,748] [INFO] Task succeeded: Blastn
[2023-06-16 19:10:52,751] [INFO] Selected 18 target genomes.
[2023-06-16 19:10:52,751] [INFO] Target genome list was writen to GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/target_genomes.txt
[2023-06-16 19:10:52,754] [INFO] Task started: fastANI
[2023-06-16 19:10:52,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgc111b407-a882-44ff-b9b6-0c03cbe8a9fb/GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna.gz --refList GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/target_genomes.txt --output GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:11:00,037] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:00,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:11:00,038] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:11:00,050] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:11:00,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:11:00,051] [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
Collinsella aerofaciens	strain=NCTC11838	GCA_900461335.1	74426	74426	type	True	94.9672	499	592	95	below_threshold
Collinsella aerofaciens	strain=JCM 10188	GCA_010509075.1	74426	74426	type	True	94.9348	498	592	95	below_threshold
Collinsella aerofaciens	strain=ATCC 25986	GCA_000169035.1	74426	74426	type	True	94.9129	504	592	95	below_threshold
Collinsella bouchesdurhonensis	strain=Marseille-P3296	GCA_900155365.1	1907654	1907654	type	True	80.6839	180	592	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	80.5151	209	592	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_000156215.1	147206	147206	type	True	80.405	207	592	95	below_threshold
Collinsella phocaeensis	strain=Marseille-P3245	GCA_900119895.1	1871016	1871016	type	True	80.0675	199	592	95	below_threshold
Collinsella intestinalis	strain=DSM 13280	GCA_000156175.1	147207	147207	suspected-type	True	80.067	181	592	95	below_threshold
Collinsella tanakaei	strain=YIT 12063	GCA_000225705.1	626935	626935	suspected-type	True	79.8673	184	592	95	below_threshold
Enorma burkinafasonensis	strain=Marseille-P9525	GCA_902150035.1	2590867	2590867	type	True	79.7079	188	592	95	below_threshold
Enorma timonensis	strain=GD5	GCA_000321165.1	1232436	1232436	type	True	79.1957	168	592	95	below_threshold
Enorma massiliensis		GCA_000311845.1	1472761	1472761	type	True	78.8629	179	592	95	below_threshold
Olsenella massiliensis	strain=SIT9	GCA_001457795.1	1622075	1622075	type	True	77.8027	85	592	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	76.5081	71	592	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:11:00,053] [INFO] DFAST Taxonomy check result was written to GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/tc_result.tsv
[2023-06-16 19:11:00,053] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:11:00,053] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:11:00,054] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference/checkm_data
[2023-06-16 19:11:00,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:11:00,081] [INFO] Task started: CheckM
[2023-06-16 19:11:00,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/checkm_input GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/checkm_result
[2023-06-16 19:11:22,771] [INFO] Task succeeded: CheckM
[2023-06-16 19:11:22,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:11:22,789] [INFO] ===== Completeness check finished =====
[2023-06-16 19:11:22,789] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:11:22,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/markers.fasta)
[2023-06-16 19:11:22,790] [INFO] Task started: Blastn
[2023-06-16 19:11:22,790] [INFO] Running command: blastn -query GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/markers.fasta -db /var/lib/cwl/stg02d256df-7491-4345-94f7-70ba6cb92c40/dqc_reference/reference_markers_gtdb.fasta -out GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:11:23,929] [INFO] Task succeeded: Blastn
[2023-06-16 19:11:23,933] [INFO] Selected 33 target genomes.
[2023-06-16 19:11:23,933] [INFO] Target genome list was writen to GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:11:23,965] [INFO] Task started: fastANI
[2023-06-16 19:11:23,965] [INFO] Running command: fastANI --query /var/lib/cwl/stgc111b407-a882-44ff-b9b6-0c03cbe8a9fb/GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna.gz --refList GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/target_genomes_gtdb.txt --output GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:11:36,522] [INFO] Task succeeded: fastANI
[2023-06-16 19:11:36,547] [INFO] Found 33 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:11:36,548] [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_900544465.1	s__Collinsella sp900544465	100.0	503	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0579	100.00	100.00	0.98	0.98	2	conclusive
GCF_015560765.1	s__Collinsella aerofaciens_M	95.0331	466	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1158	96.04	95.15	0.86	0.78	15	-
GCF_010509075.1	s__Collinsella aerofaciens	94.9348	498	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.99	99.98	1.00	0.99	4	-
GCA_900549745.1	s__Collinsella sp900549745	94.9162	419	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1078	95.40	95.40	0.87	0.87	2	-
GCA_008671135.1	s__Collinsella aerofaciens_J	94.9093	474	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.2147	97.21	95.28	0.90	0.82	6	-
GCA_018382125.1	s__Collinsella sp018382125	94.8224	469	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1759	N/A	N/A	N/A	N/A	1	-
GCA_900543515.1	s__Collinsella sp900543515	94.8108	447	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.1148	100.00	100.00	0.98	0.98	2	-
GCA_900541235.1	s__Collinsella sp900541235	94.7761	472	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.02	95.02	0.86	0.86	2	-
GCA_018380195.1	s__Collinsella sp018380195	94.5746	469	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.09	95.09	0.91	0.91	2	-
GCA_000434535.1	s__Collinsella sp000434535	94.5619	394	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541885.1	s__Collinsella sp900541885	94.5613	473	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900545605.1	s__Collinsella sp900545605	94.5498	430	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549655.1	s__Collinsella sp900549655	94.509	403	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.97	0.97	2	-
GCA_900541205.1	s__Collinsella sp900541205	94.5053	482	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.97	99.97	0.98	0.98	2	-
GCA_900759565.1	s__Collinsella sp900759565	94.4592	437	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.12	95.02	0.84	0.84	3	-
GCA_900544425.1	s__Collinsella sp900544425	94.4206	390	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900540895.1	s__Collinsella sp900540895	94.3472	453	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	95.25	95.25	0.87	0.87	2	-
GCA_900761085.1	s__Collinsella sp900761085	94.3061	394	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900760245.1	s__Collinsella sp900760245	94.246	406	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541025.1	s__Collinsella sp900541025	94.2091	465	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553475.1	s__Collinsella sp900553475	94.1436	328	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0051	N/A	N/A	N/A	N/A	1	-
GCA_900551305.1	s__Collinsella sp900551305	94.1027	332	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0792	96.10	95.39	0.89	0.68	9	-
GCA_900550355.1	s__Collinsella sp900550355	94.0826	378	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.039	N/A	N/A	N/A	N/A	1	-
GCA_905204635.1	s__Collinsella sp905204635	94.0788	334	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018368345.1	s__Collinsella sp018368345	94.0307	465	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546455.1	s__Collinsella sp900546455	93.8869	440	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900545995.1	s__Collinsella sp900545995	93.7889	394	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754385.1	s__Collinsella sp900754385	93.7563	303	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	99.42	99.42	0.88	0.88	2	-
GCA_900553165.1	s__Collinsella sp900553165	93.6804	291	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555765.1	s__Collinsella sp900555765	93.5055	280	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900761945.1	s__Collinsella sp900761945	93.0988	304	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556705.1	s__Collinsella sp900556705	92.8437	252	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761145.1	s__Collinsella sp900761145	92.8195	413	592	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 19:11:36,550] [INFO] GTDB search result was written to GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/result_gtdb.tsv
[2023-06-16 19:11:36,550] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:11:36,555] [INFO] DFAST_QC result json was written to GCA_905208435.1_SRR2912784-mag-bin.9_genomic.fna/dqc_result.json
[2023-06-16 19:11:36,556] [INFO] DFAST_QC completed!
[2023-06-16 19:11:36,556] [INFO] Total running time: 0h0m52s