[2023-06-29 00:38:16,177] [INFO] DFAST_QC pipeline started.
[2023-06-29 00:38:16,178] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 00:38:16,179] [INFO] DQC Reference Directory: /var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference
[2023-06-29 00:38:18,731] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 00:38:18,732] [INFO] Task started: Prodigal
[2023-06-29 00:38:18,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg56b84204-3f58-4865-b500-9ea7759efb9b/GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 00:38:25,477] [INFO] Task succeeded: Prodigal
[2023-06-29 00:38:25,478] [INFO] Task started: HMMsearch
[2023-06-29 00:38:25,478] [INFO] Running command: hmmsearch --tblout GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference/reference_markers.hmm GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 00:38:25,718] [INFO] Task succeeded: HMMsearch
[2023-06-29 00:38:25,720] [INFO] Found 6/6 markers.
[2023-06-29 00:38:25,751] [INFO] Query marker FASTA was written to GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 00:38:25,752] [INFO] Task started: Blastn
[2023-06-29 00:38:25,752] [INFO] Running command: blastn -query GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference/reference_markers.fasta -out GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:38:26,333] [INFO] Task succeeded: Blastn
[2023-06-29 00:38:26,339] [INFO] Selected 26 target genomes.
[2023-06-29 00:38:26,339] [INFO] Target genome list was writen to GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 00:38:26,340] [INFO] Task started: fastANI
[2023-06-29 00:38:26,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b84204-3f58-4865-b500-9ea7759efb9b/GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 00:38:39,945] [INFO] Task succeeded: fastANI
[2023-06-29 00:38:39,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 00:38:39,946] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 00:38:39,963] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 00:38:39,963] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 00:38:39,963] [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
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	77.4822	147	919	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.4801	135	919	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	77.4801	148	919	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.434	133	919	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_008281175.1	89153	89153	type	True	77.4023	132	919	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.3326	123	919	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.1495	56	919	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.0928	103	919	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.0431	104	919	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	76.9665	73	919	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	76.8289	59	919	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_025148285.1	168384	168384	type	True	76.6451	57	919	95	below_threshold
Marvinbryantia formatexigens	strain=I-52	GCA_900102475.1	168384	168384	type	True	76.6451	57	919	95	below_threshold
Marvinbryantia formatexigens	strain=DSM 14469	GCA_000173815.1	168384	168384	type	True	76.6402	56	919	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	76.6042	87	919	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	76.5388	63	919	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 00:38:39,966] [INFO] DFAST Taxonomy check result was written to GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 00:38:39,966] [INFO] ===== Taxonomy check completed =====
[2023-06-29 00:38:39,966] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 00:38:39,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference/checkm_data
[2023-06-29 00:38:39,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 00:38:40,003] [INFO] Task started: CheckM
[2023-06-29 00:38:40,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 00:39:06,036] [INFO] Task succeeded: CheckM
[2023-06-29 00:39:06,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 00:39:06,064] [INFO] ===== Completeness check finished =====
[2023-06-29 00:39:06,065] [INFO] ===== Start GTDB Search =====
[2023-06-29 00:39:06,065] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 00:39:06,065] [INFO] Task started: Blastn
[2023-06-29 00:39:06,066] [INFO] Running command: blastn -query GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc235c9b5-df22-466c-8bdb-46962cd325ba/dqc_reference/reference_markers_gtdb.fasta -out GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 00:39:06,860] [INFO] Task succeeded: Blastn
[2023-06-29 00:39:06,865] [INFO] Selected 10 target genomes.
[2023-06-29 00:39:06,865] [INFO] Target genome list was writen to GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 00:39:06,873] [INFO] Task started: fastANI
[2023-06-29 00:39:06,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg56b84204-3f58-4865-b500-9ea7759efb9b/GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 00:39:13,676] [INFO] Task succeeded: fastANI
[2023-06-29 00:39:13,690] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 00:39:13,690] [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_000403475.2	s__MD308 sp000403475	97.7074	848	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	98.66	98.66	0.92	0.92	2	conclusive
GCA_910578455.1	s__MD308 sp910578455	87.7509	466	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586965.1	s__MD308 sp910586965	85.7533	699	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575105.1	s__MD308 sp910575105	82.3268	567	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	99.99	99.99	0.99	0.99	2	-
GCA_010206225.2	s__MD308 sp010206225	80.78	462	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	98.71	98.71	0.87	0.87	2	-
GCA_910579335.1	s__MD308 sp910579335	80.5698	434	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584615.1	s__MD308 sp910584615	80.4676	444	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910580235.1	s__UBA7109 sp910580235	77.5866	126	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002492335.1	s__UBA7109 sp002492335	77.4196	93	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549995.1	s__UMGS1251 sp900549995	76.3212	65	919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1251	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 00:39:13,692] [INFO] GTDB search result was written to GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 00:39:13,693] [INFO] ===== GTDB Search completed =====
[2023-06-29 00:39:13,697] [INFO] DFAST_QC result json was written to GCA_948439895.1_SRR18243795_bin.23_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 00:39:13,698] [INFO] DFAST_QC completed!
[2023-06-29 00:39:13,698] [INFO] Total running time: 0h0m58s