[2023-06-08 19:34:41,019] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:34:41,021] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:34:41,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference
[2023-06-08 19:34:42,254] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:34:42,255] [INFO] Task started: Prodigal
[2023-06-08 19:34:42,256] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a65213c-876f-442e-9937-c7d4094fbeaa/GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:34:47,261] [INFO] Task succeeded: Prodigal
[2023-06-08 19:34:47,262] [INFO] Task started: HMMsearch
[2023-06-08 19:34:47,262] [INFO] Running command: hmmsearch --tblout GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference/reference_markers.hmm GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:34:47,479] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:34:47,480] [INFO] Found 6/6 markers.
[2023-06-08 19:34:47,505] [INFO] Query marker FASTA was written to GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:34:47,505] [INFO] Task started: Blastn
[2023-06-08 19:34:47,506] [INFO] Running command: blastn -query GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference/reference_markers.fasta -out GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:34:48,161] [INFO] Task succeeded: Blastn
[2023-06-08 19:34:48,165] [INFO] Selected 22 target genomes.
[2023-06-08 19:34:48,165] [INFO] Target genome list was writen to GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:34:48,167] [INFO] Task started: fastANI
[2023-06-08 19:34:48,167] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a65213c-876f-442e-9937-c7d4094fbeaa/GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:34:57,643] [INFO] Task succeeded: fastANI
[2023-06-08 19:34:57,644] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:34:57,644] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:34:57,665] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:34:57,665] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:34:57,665] [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
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	80.1485	242	689	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.0891	103	689	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	78.0119	106	689	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.9818	184	689	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	77.9517	180	689	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	77.8322	133	689	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.8199	146	689	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.8162	132	689	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.7742	145	689	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	77.6693	142	689	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.6415	118	689	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.599	101	689	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.5843	136	689	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.5617	142	689	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.4674	106	689	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	77.3992	83	689	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.3978	126	689	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.3966	126	689	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.2114	119	689	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	76.9672	61	689	95	below_threshold
Sellimonas intestinalis	strain=BR72	GCA_001280875.1	1653434	1653434	type	True	76.9393	77	689	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:34:57,667] [INFO] DFAST Taxonomy check result was written to GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:34:57,668] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:34:57,668] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:34:57,668] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference/checkm_data
[2023-06-08 19:34:57,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:34:57,698] [INFO] Task started: CheckM
[2023-06-08 19:34:57,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:35:19,861] [INFO] Task succeeded: CheckM
[2023-06-08 19:35:19,862] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:35:19,882] [INFO] ===== Completeness check finished =====
[2023-06-08 19:35:19,882] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:35:19,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:35:19,883] [INFO] Task started: Blastn
[2023-06-08 19:35:19,883] [INFO] Running command: blastn -query GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6df9bd1e-1fed-474f-b6eb-3a490754f20b/dqc_reference/reference_markers_gtdb.fasta -out GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:35:20,966] [INFO] Task succeeded: Blastn
[2023-06-08 19:35:20,972] [INFO] Selected 16 target genomes.
[2023-06-08 19:35:20,972] [INFO] Target genome list was writen to GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:35:20,975] [INFO] Task started: fastANI
[2023-06-08 19:35:20,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a65213c-876f-442e-9937-c7d4094fbeaa/GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:35:28,732] [INFO] Task succeeded: fastANI
[2023-06-08 19:35:28,746] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:35:28,746] [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_000433535.1	s__CAG-317 sp000433535	97.8553	585	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	conclusive
GCA_900543415.1	s__CAG-317 sp900543415	94.2201	553	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	97.35	95.87	0.87	0.78	4	-
GCF_900240315.1	s__Dorea_B phocaeensis	80.1439	241	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCF_003435815.1	s__CAG-317 sp000433215	78.8849	207	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_910578495.1	s__CAG-317 sp910578495	78.4925	250	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578865.1	s__CAG-317 sp011960265	78.2734	185	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	99.18	99.18	0.88	0.88	2	-
GCA_016295505.1	s__Dorea_A sp016295505	77.9791	135	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154065.1	s__Dorea_A longicatena	77.9517	180	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCF_001404875.1	s__Dorea_A longicatena_B	77.9132	180	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCA_900550865.1	s__Dorea_A sp900550865	77.8811	146	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295125.1	s__Clostridium_AP scindens	77.8322	133	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.44	99.12	0.90	0.78	13	-
GCA_000509125.1	s__Clostridium_AP sp000509125	77.7722	131	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_AP	95.0	99.12	98.62	0.95	0.91	5	-
GCA_002492335.1	s__UBA7109 sp002492335	77.6964	113	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	77.604	121	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_900553355.1	s__Merdimonas sp900553355	77.4686	135	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575605.1	s__UBA7109 sp910575605	77.4163	123	689	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.27	99.27	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-06-08 19:35:28,748] [INFO] GTDB search result was written to GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:35:28,749] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:35:28,753] [INFO] DFAST_QC result json was written to GCA_947003085.1_SRR19721642_bin.4_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:35:28,753] [INFO] DFAST_QC completed!
[2023-06-08 19:35:28,753] [INFO] Total running time: 0h0m48s