[2023-06-08 03:42:58,856] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:58,857] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:58,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference
[2023-06-08 03:43:00,051] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:43:00,052] [INFO] Task started: Prodigal
[2023-06-08 03:43:00,052] [INFO] Running command: gunzip -c /var/lib/cwl/stga8d986e9-45c6-428f-a468-8b7a2013bbfb/GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:43:07,248] [INFO] Task succeeded: Prodigal
[2023-06-08 03:43:07,248] [INFO] Task started: HMMsearch
[2023-06-08 03:43:07,249] [INFO] Running command: hmmsearch --tblout GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference/reference_markers.hmm GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:43:07,472] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:43:07,473] [INFO] Found 6/6 markers.
[2023-06-08 03:43:07,501] [INFO] Query marker FASTA was written to GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 03:43:07,502] [INFO] Task started: Blastn
[2023-06-08 03:43:07,502] [INFO] Running command: blastn -query GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference/reference_markers.fasta -out GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:43:08,108] [INFO] Task succeeded: Blastn
[2023-06-08 03:43:08,111] [INFO] Selected 26 target genomes.
[2023-06-08 03:43:08,111] [INFO] Target genome list was writen to GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 03:43:08,115] [INFO] Task started: fastANI
[2023-06-08 03:43:08,115] [INFO] Running command: fastANI --query /var/lib/cwl/stga8d986e9-45c6-428f-a468-8b7a2013bbfb/GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:43:22,075] [INFO] Task succeeded: fastANI
[2023-06-08 03:43:22,075] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:43:22,075] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:43:22,082] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:43:22,083] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 03:43:22,083] [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
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.745	68	1085	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.7115	69	1085	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.6332	61	1085	95	below_threshold
Lacrimispora celerecrescens	strain=18A	GCA_002797975.1	29354	29354	type	True	76.5224	70	1085	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.4067	69	1085	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.277	65	1085	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 03:43:22,084] [INFO] DFAST Taxonomy check result was written to GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 03:43:22,085] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:43:22,085] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:43:22,085] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference/checkm_data
[2023-06-08 03:43:22,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:43:22,119] [INFO] Task started: CheckM
[2023-06-08 03:43:22,120] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 03:43:48,496] [INFO] Task succeeded: CheckM
[2023-06-08 03:43:48,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:43:48,513] [INFO] ===== Completeness check finished =====
[2023-06-08 03:43:48,514] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:43:48,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 03:43:48,514] [INFO] Task started: Blastn
[2023-06-08 03:43:48,515] [INFO] Running command: blastn -query GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgecd9e628-601a-4a55-9be3-8bd01166fe0c/dqc_reference/reference_markers_gtdb.fasta -out GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:43:49,498] [INFO] Task succeeded: Blastn
[2023-06-08 03:43:49,501] [INFO] Selected 21 target genomes.
[2023-06-08 03:43:49,501] [INFO] Target genome list was writen to GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:43:49,506] [INFO] Task started: fastANI
[2023-06-08 03:43:49,507] [INFO] Running command: fastANI --query /var/lib/cwl/stga8d986e9-45c6-428f-a468-8b7a2013bbfb/GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:44:02,418] [INFO] Task succeeded: fastANI
[2023-06-08 03:44:02,432] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:44:02,432] [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_002358555.1	s__UBA3402 sp002358555	99.0959	741	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	98.83	98.83	0.87	0.87	2	conclusive
GCA_910574345.1	s__UBA3402 sp910574345	77.9985	240	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575585.1	s__UBA3402 sp910575585	77.6307	198	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	99.89	99.85	0.96	0.96	3	-
GCA_910585645.1	s__UBA3402 sp910585645	77.6256	176	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588865.1	s__UBA3402 sp910588865	77.5323	166	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588505.1	s__UBA3402 sp910588505	77.282	162	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586845.1	s__UBA3402 sp910586845	77.2749	160	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585435.1	s__UBA3402 sp910585435	77.1334	115	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579515.1	s__UBA3402 sp910579515	77.1327	146	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002899675.1	s__CHH4-2 sp002899675	76.8944	84	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	100.00	100.00	0.98	0.98	2	-
GCA_018378255.1	s__CHH4-2 sp018378255	76.8798	78	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CHH4-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900538475.1	s__Ventrimonas sp900538475	76.844	101	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCA_900105215.1	s__Lacrimispora sphenoides_A	76.7307	69	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	96.8556	97.72	97.62	0.92	0.89	4	-
GCA_902363735.1	s__Lacrimispora sp902363735	76.5453	77	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lacrimispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588325.1	s__UBA3402 sp910588325	76.4435	143	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240245.1	s__Lachnoclostridium_A edouardi	76.4274	91	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900542035.1	s__UMGS1370 sp900542035	76.263	68	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1370	95.0	99.54	99.09	0.95	0.91	3	-
GCA_905215625.1	s__UMGS1370 sp905215625	76.1418	58	1085	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1370	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:44:02,434] [INFO] GTDB search result was written to GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 03:44:02,434] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:44:02,437] [INFO] DFAST_QC result json was written to GCA_947428385.1_SRR12506352_bin.3_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 03:44:02,438] [INFO] DFAST_QC completed!
[2023-06-08 03:44:02,438] [INFO] Total running time: 0h1m4s