[2023-06-04 20:37:32,650] [INFO] DFAST_QC pipeline started.
[2023-06-04 20:37:32,660] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 20:37:32,660] [INFO] DQC Reference Directory: /var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference
[2023-06-04 20:37:34,581] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 20:37:34,582] [INFO] Task started: Prodigal
[2023-06-04 20:37:34,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d16012b-99e4-483a-a5fd-4bd57f8a4cd1/GCA_934845665.1_MTG234_bin.25.fa_genomic.fna.gz | prodigal -d GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/cds.fna -a GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 20:37:39,877] [INFO] Task succeeded: Prodigal
[2023-06-04 20:37:39,877] [INFO] Task started: HMMsearch
[2023-06-04 20:37:39,878] [INFO] Running command: hmmsearch --tblout GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference/reference_markers.hmm GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/protein.faa > /dev/null
[2023-06-04 20:37:40,114] [INFO] Task succeeded: HMMsearch
[2023-06-04 20:37:40,116] [INFO] Found 6/6 markers.
[2023-06-04 20:37:40,157] [INFO] Query marker FASTA was written to GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/markers.fasta
[2023-06-04 20:37:40,157] [INFO] Task started: Blastn
[2023-06-04 20:37:40,157] [INFO] Running command: blastn -query GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference/reference_markers.fasta -out GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:37:40,796] [INFO] Task succeeded: Blastn
[2023-06-04 20:37:40,800] [INFO] Selected 20 target genomes.
[2023-06-04 20:37:40,800] [INFO] Target genome list was writen to GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/target_genomes.txt
[2023-06-04 20:37:40,803] [INFO] Task started: fastANI
[2023-06-04 20:37:40,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d16012b-99e4-483a-a5fd-4bd57f8a4cd1/GCA_934845665.1_MTG234_bin.25.fa_genomic.fna.gz --refList GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/target_genomes.txt --output GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 20:37:51,090] [INFO] Task succeeded: fastANI
[2023-06-04 20:37:51,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 20:37:51,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 20:37:51,105] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2023-06-04 20:37:51,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-04 20:37:51,106] [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
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	98.2063	546	615	95	conclusive
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.1117	60	615	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.0281	76	615	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.0237	75	615	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.7254	70	615	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	77.4844	101	615	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.2216	86	615	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	77.0877	53	615	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.9499	65	615	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	76.9337	73	615	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.7983	65	615	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.7828	56	615	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.7657	66	615	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.7509	66	615	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 20:37:51,111] [INFO] DFAST Taxonomy check result was written to GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/tc_result.tsv
[2023-06-04 20:37:51,113] [INFO] ===== Taxonomy check completed =====
[2023-06-04 20:37:51,113] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 20:37:51,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference/checkm_data
[2023-06-04 20:37:51,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 20:37:51,149] [INFO] Task started: CheckM
[2023-06-04 20:37:51,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/checkm_input GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/checkm_result
[2023-06-04 20:38:15,137] [INFO] Task succeeded: CheckM
[2023-06-04 20:38:15,138] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.60%
Contamintation: 4.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 20:38:15,168] [INFO] ===== Completeness check finished =====
[2023-06-04 20:38:15,168] [INFO] ===== Start GTDB Search =====
[2023-06-04 20:38:15,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/markers.fasta)
[2023-06-04 20:38:15,169] [INFO] Task started: Blastn
[2023-06-04 20:38:15,169] [INFO] Running command: blastn -query GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg5eb78dc6-dcf3-48df-8d74-e55043303282/dqc_reference/reference_markers_gtdb.fasta -out GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 20:38:16,029] [INFO] Task succeeded: Blastn
[2023-06-04 20:38:16,034] [INFO] Selected 16 target genomes.
[2023-06-04 20:38:16,035] [INFO] Target genome list was writen to GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 20:38:16,068] [INFO] Task started: fastANI
[2023-06-04 20:38:16,069] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d16012b-99e4-483a-a5fd-4bd57f8a4cd1/GCA_934845665.1_MTG234_bin.25.fa_genomic.fna.gz --refList GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 20:38:24,586] [INFO] Task succeeded: fastANI
[2023-06-04 20:38:24,603] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 20:38:24,604] [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_902363685.1	s__UMGS1375 sp900066615	98.317	559	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	98.15	97.87	0.85	0.79	16	conclusive
GCA_900551235.1	s__UMGS1375 sp900551235	87.2436	369	615	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_905214675.1	s__UMGS1375 sp905214675	86.8416	296	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003461955.1	s__Blautia_A sp900066335	77.6365	76	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCA_900544685.1	s__Marvinbryantia sp900544685	77.4743	74	615	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_003122485.1	s__Eubacterium_I ramulus_A	77.4011	68	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.76	98.61	0.82	0.80	7	-
GCA_900551715.1	s__Blautia_A sp900551715	77.2278	60	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000469345.1	s__Eubacterium_I ramulus	77.0411	68	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.54	98.22	0.85	0.78	13	-
GCF_003463065.1	s__Limivivens sp900066135	77.0123	102	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.47	97.63	0.91	0.79	5	-
GCF_003481825.1	s__Ventrimonas sp003481825	76.904	54	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.33	98.65	0.93	0.87	3	-
GCF_003435815.1	s__CAG-317 sp000433215	76.8881	69	615	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_003612585.1	s__Choladousia sp003612585	76.8507	52	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539525.1	s__CAG-56 sp900539525	76.7818	101	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.91	99.91	0.93	0.93	2	-
GCF_008121495.1	s__Ruminococcus_B gnavus	76.7657	66	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	98.58	96.13	0.80	0.66	102	-
GCA_018365455.1	s__Robinsoniella sp900555455	76.1816	61	615	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Robinsoniella	95.0	99.95	99.95	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-04 20:38:24,605] [INFO] GTDB search result was written to GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/result_gtdb.tsv
[2023-06-04 20:38:24,606] [INFO] ===== GTDB Search completed =====
[2023-06-04 20:38:24,610] [INFO] DFAST_QC result json was written to GCA_934845665.1_MTG234_bin.25.fa_genomic.fna/dqc_result.json
[2023-06-04 20:38:24,610] [INFO] DFAST_QC completed!
[2023-06-04 20:38:24,610] [INFO] Total running time: 0h0m52s