[2023-06-05 05:55:40,735] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:55:40,737] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:55:40,738] [INFO] DQC Reference Directory: /var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference
[2023-06-05 05:55:43,089] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:55:43,090] [INFO] Task started: Prodigal
[2023-06-05 05:55:43,091] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7014e4a-6c25-4460-8f2d-e16501d1c128/GCA_934838045.1_MTG229_bin.39.fa_genomic.fna.gz | prodigal -d GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/cds.fna -a GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:55:49,994] [INFO] Task succeeded: Prodigal
[2023-06-05 05:55:49,995] [INFO] Task started: HMMsearch
[2023-06-05 05:55:49,995] [INFO] Running command: hmmsearch --tblout GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference/reference_markers.hmm GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:55:50,245] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:55:50,246] [INFO] Found 6/6 markers.
[2023-06-05 05:55:50,281] [INFO] Query marker FASTA was written to GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/markers.fasta
[2023-06-05 05:55:50,282] [INFO] Task started: Blastn
[2023-06-05 05:55:50,282] [INFO] Running command: blastn -query GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference/reference_markers.fasta -out GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:55:50,935] [INFO] Task succeeded: Blastn
[2023-06-05 05:55:50,940] [INFO] Selected 23 target genomes.
[2023-06-05 05:55:50,941] [INFO] Target genome list was writen to GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/target_genomes.txt
[2023-06-05 05:55:50,942] [INFO] Task started: fastANI
[2023-06-05 05:55:50,942] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7014e4a-6c25-4460-8f2d-e16501d1c128/GCA_934838045.1_MTG229_bin.39.fa_genomic.fna.gz --refList GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/target_genomes.txt --output GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:56:03,062] [INFO] Task succeeded: fastANI
[2023-06-05 05:56:03,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:56:03,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:56:03,092] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2023-06-05 05:56:03,092] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 05:56:03,093] [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	98.599	791	890	95	conclusive
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	78.4129	115	890	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	78.3826	115	890	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.0034	141	890	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	78.001	92	890	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	77.8829	121	890	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.6444	130	890	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.495	109	890	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.356	102	890	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	77.3489	57	890	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.2096	105	890	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.1955	107	890	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.1739	106	890	95	below_threshold
Murimonas intestini	strain=DSM 26524	GCA_024622195.1	1337051	1337051	type	True	76.9825	76	890	95	below_threshold
Blautia marasmi	strain=Marseille-P2377	GCA_900258535.1	1917868	1917868	suspected-type	True	76.7302	83	890	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	76.696	84	890	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.6274	55	890	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.5842	79	890	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.5265	69	890	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	76.5216	72	890	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	76.3064	65	890	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	76.0931	65	890	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:56:03,095] [INFO] DFAST Taxonomy check result was written to GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/tc_result.tsv
[2023-06-05 05:56:03,095] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:56:03,095] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:56:03,096] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference/checkm_data
[2023-06-05 05:56:03,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:56:03,126] [INFO] Task started: CheckM
[2023-06-05 05:56:03,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/checkm_input GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/checkm_result
[2023-06-05 05:56:30,760] [INFO] Task succeeded: CheckM
[2023-06-05 05:56:30,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 2.56%
Strain heterogeneity: 20.00%
--------------------------------------------------------------------------------
[2023-06-05 05:56:30,788] [INFO] ===== Completeness check finished =====
[2023-06-05 05:56:30,789] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:56:30,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/markers.fasta)
[2023-06-05 05:56:30,790] [INFO] Task started: Blastn
[2023-06-05 05:56:30,790] [INFO] Running command: blastn -query GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stgaed9a211-91ef-4289-a382-a9a86005b4be/dqc_reference/reference_markers_gtdb.fasta -out GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:56:31,863] [INFO] Task succeeded: Blastn
[2023-06-05 05:56:31,867] [INFO] Selected 20 target genomes.
[2023-06-05 05:56:31,868] [INFO] Target genome list was writen to GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:56:31,868] [INFO] Task started: fastANI
[2023-06-05 05:56:31,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7014e4a-6c25-4460-8f2d-e16501d1c128/GCA_934838045.1_MTG229_bin.39.fa_genomic.fna.gz --refList GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:56:43,478] [INFO] Task succeeded: fastANI
[2023-06-05 05:56:43,495] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:56:43,495] [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	98.3946	797	890	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	87.3081	512	890	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	87.1806	390	890	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_902363665.1	s__Choladousia sp902363665	78.5652	144	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Choladousia	95.0	97.59	97.59	0.93	0.93	2	-
GCF_000153905.1	s__Blautia_A obeum	78.4129	115	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.25	97.20	0.82	0.75	45	-
GCA_905214955.1	s__Limivivens sp905214955	78.2934	148	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900066355.1	s__Blautia_A sp900066355	77.8709	134	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.38	98.38	0.93	0.93	2	-
GCF_009883055.1	s__Blautia_A sp900548245	77.7294	134	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.63	98.37	0.88	0.85	5	-
GCA_018223435.1	s__Limivivens sp900543575	77.6833	125	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Limivivens	95.0	98.02	97.88	0.92	0.90	4	-
GCF_003481825.1	s__Ventrimonas sp003481825	77.6181	81	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.33	98.65	0.93	0.87	3	-
GCA_000155875.1	s__Bariatricus comes	77.5879	127	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCF_003122485.1	s__Eubacterium_I ramulus_A	77.4966	117	890	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_900544685.1	s__Marvinbryantia sp900544685	77.4158	119	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Marvinbryantia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551715.1	s__Blautia_A sp900551715	77.3721	88	890	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	-
GCA_900539525.1	s__CAG-56 sp900539525	77.3326	131	890	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	77.1739	106	890	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_900541985.1	s__Blautia_A sp900541985	77.1617	90	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.92	99.92	0.93	0.93	2	-
GCF_003435815.1	s__CAG-317 sp000433215	77.1276	100	890	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_900762665.1	s__CAG-56 sp900762665	76.5856	62	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-56	95.0	99.95	99.95	0.93	0.93	2	-
GCA_902782995.1	s__RUG115 sp902782995	76.3037	64	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:56:43,497] [INFO] GTDB search result was written to GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/result_gtdb.tsv
[2023-06-05 05:56:43,497] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:56:43,502] [INFO] DFAST_QC result json was written to GCA_934838045.1_MTG229_bin.39.fa_genomic.fna/dqc_result.json
[2023-06-05 05:56:43,502] [INFO] DFAST_QC completed!
[2023-06-05 05:56:43,502] [INFO] Total running time: 0h1m3s