[2023-06-16 19:07:45,057] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:07:45,060] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:07:45,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference
[2023-06-16 19:07:46,392] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:07:46,393] [INFO] Task started: Prodigal
[2023-06-16 19:07:46,393] [INFO] Running command: gunzip -c /var/lib/cwl/stg26f899a0-32eb-43f8-ab6b-eedaf2c47121/GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna.gz | prodigal -d GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/cds.fna -a GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:07:53,305] [INFO] Task succeeded: Prodigal
[2023-06-16 19:07:53,305] [INFO] Task started: HMMsearch
[2023-06-16 19:07:53,305] [INFO] Running command: hmmsearch --tblout GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference/reference_markers.hmm GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:07:53,608] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:07:53,615] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg26f899a0-32eb-43f8-ab6b-eedaf2c47121/GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna.gz]
[2023-06-16 19:07:53,644] [INFO] Query marker FASTA was written to GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/markers.fasta
[2023-06-16 19:07:53,644] [INFO] Task started: Blastn
[2023-06-16 19:07:53,644] [INFO] Running command: blastn -query GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference/reference_markers.fasta -out GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:07:54,285] [INFO] Task succeeded: Blastn
[2023-06-16 19:07:54,290] [INFO] Selected 16 target genomes.
[2023-06-16 19:07:54,290] [INFO] Target genome list was writen to GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/target_genomes.txt
[2023-06-16 19:07:54,295] [INFO] Task started: fastANI
[2023-06-16 19:07:54,296] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f899a0-32eb-43f8-ab6b-eedaf2c47121/GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna.gz --refList GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/target_genomes.txt --output GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:08:03,774] [INFO] Task succeeded: fastANI
[2023-06-16 19:08:03,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:08:03,775] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:08:03,788] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:08:03,788] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:08:03,788] [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
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	82.0906	513	896	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	82.0529	503	896	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	81.909	500	896	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.3382	288	896	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.104	295	896	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.0092	283	896	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	78.9357	296	896	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	78.4944	264	896	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.2339	83	896	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.0758	76	896	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.9378	80	896	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.7898	84	896	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	76.4281	66	896	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.2278	57	896	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	76.0532	59	896	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:08:03,803] [INFO] DFAST Taxonomy check result was written to GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/tc_result.tsv
[2023-06-16 19:08:03,803] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:08:03,804] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:08:03,804] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference/checkm_data
[2023-06-16 19:08:03,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:08:03,845] [INFO] Task started: CheckM
[2023-06-16 19:08:03,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/checkm_input GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/checkm_result
[2023-06-16 19:08:31,522] [INFO] Task succeeded: CheckM
[2023-06-16 19:08:31,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:08:31,565] [INFO] ===== Completeness check finished =====
[2023-06-16 19:08:31,565] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:08:31,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/markers.fasta)
[2023-06-16 19:08:31,566] [INFO] Task started: Blastn
[2023-06-16 19:08:31,566] [INFO] Running command: blastn -query GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeccfe52-5703-45ec-816c-5abdaecd8ff5/dqc_reference/reference_markers_gtdb.fasta -out GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:08:32,623] [INFO] Task succeeded: Blastn
[2023-06-16 19:08:32,627] [INFO] Selected 11 target genomes.
[2023-06-16 19:08:32,627] [INFO] Target genome list was writen to GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:08:32,648] [INFO] Task started: fastANI
[2023-06-16 19:08:32,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f899a0-32eb-43f8-ab6b-eedaf2c47121/GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna.gz --refList GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/target_genomes_gtdb.txt --output GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:08:41,268] [INFO] Task succeeded: fastANI
[2023-06-16 19:08:41,278] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 19:08:41,278] [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
GCF_003461245.1	s__Blautia_A sp000436615	98.772	827	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.75	98.36	0.88	0.81	8	conclusive
GCF_009883055.1	s__Blautia_A sp900548245	85.7537	659	896	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	-
GCF_018918125.1	s__Blautia_A sp018918125	84.1965	524	896	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_900751995.1	s__Blautia_A sp900751995	82.9838	271	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	95.05	95.05	0.55	0.55	2	-
GCA_900066355.1	s__Blautia_A sp900066355	82.2641	515	896	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_000153905.1	s__Blautia_A obeum	82.0495	503	896	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	-
GCF_000210015.1	s__Blautia_A obeum_B	81.7887	497	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.64	98.44	0.85	0.84	7	-
GCF_900120195.1	s__Blautia_A sp900120195	81.6151	497	896	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.52	98.42	0.85	0.83	5	-
GCA_900551715.1	s__Blautia_A sp900551715	79.7701	368	896	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_900764225.1	s__Blautia_A sp900764225	78.6798	237	896	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_900541985.1	s__Blautia_A sp900541985	78.6078	237	896	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	-
--------------------------------------------------------------------------------
[2023-06-16 19:08:41,280] [INFO] GTDB search result was written to GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/result_gtdb.tsv
[2023-06-16 19:08:41,281] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:08:41,289] [INFO] DFAST_QC result json was written to GCA_905202875.1_ERR1430509-mag-bin.16_genomic.fna/dqc_result.json
[2023-06-16 19:08:41,289] [INFO] DFAST_QC completed!
[2023-06-16 19:08:41,289] [INFO] Total running time: 0h0m56s