[2023-06-17 01:33:32,717] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:33:32,723] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:33:32,723] [INFO] DQC Reference Directory: /var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference
[2023-06-17 01:33:34,022] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:33:34,023] [INFO] Task started: Prodigal
[2023-06-17 01:33:34,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f121296-04aa-4655-92d0-18a01bd46616/GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna.gz | prodigal -d GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/cds.fna -a GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:33:40,471] [INFO] Task succeeded: Prodigal
[2023-06-17 01:33:40,472] [INFO] Task started: HMMsearch
[2023-06-17 01:33:40,472] [INFO] Running command: hmmsearch --tblout GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference/reference_markers.hmm GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:33:40,733] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:33:40,734] [INFO] Found 6/6 markers.
[2023-06-17 01:33:40,764] [INFO] Query marker FASTA was written to GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/markers.fasta
[2023-06-17 01:33:40,764] [INFO] Task started: Blastn
[2023-06-17 01:33:40,764] [INFO] Running command: blastn -query GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/markers.fasta -db /var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference/reference_markers.fasta -out GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:33:41,427] [INFO] Task succeeded: Blastn
[2023-06-17 01:33:41,432] [INFO] Selected 16 target genomes.
[2023-06-17 01:33:41,433] [INFO] Target genome list was writen to GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/target_genomes.txt
[2023-06-17 01:33:41,435] [INFO] Task started: fastANI
[2023-06-17 01:33:41,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f121296-04aa-4655-92d0-18a01bd46616/GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna.gz --refList GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/target_genomes.txt --output GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:33:50,256] [INFO] Task succeeded: fastANI
[2023-06-17 01:33:50,257] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:33:50,257] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:33:50,276] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-06-17 01:33:50,276] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 01:33:50,276] [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
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	98.3676	725	839	95	conclusive
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	98.363	736	839	95	conclusive
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	79.7108	169	839	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.8707	107	839	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.399	169	839	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	78.3532	100	839	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	78.2734	125	839	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.0313	55	839	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.7484	115	839	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.7469	84	839	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.6833	113	839	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	77.666	91	839	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.5847	107	839	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.4911	59	839	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.284	106	839	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.2262	72	839	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:33:50,278] [INFO] DFAST Taxonomy check result was written to GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/tc_result.tsv
[2023-06-17 01:33:50,279] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:33:50,279] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:33:50,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference/checkm_data
[2023-06-17 01:33:50,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:33:50,308] [INFO] Task started: CheckM
[2023-06-17 01:33:50,308] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/checkm_input GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/checkm_result
[2023-06-17 01:34:16,342] [INFO] Task succeeded: CheckM
[2023-06-17 01:34:16,343] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 01:34:16,364] [INFO] ===== Completeness check finished =====
[2023-06-17 01:34:16,365] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:34:16,365] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/markers.fasta)
[2023-06-17 01:34:16,365] [INFO] Task started: Blastn
[2023-06-17 01:34:16,366] [INFO] Running command: blastn -query GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/markers.fasta -db /var/lib/cwl/stg4221bc14-73d8-48c8-8e2a-aeac2f1e46f3/dqc_reference/reference_markers_gtdb.fasta -out GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:34:17,431] [INFO] Task succeeded: Blastn
[2023-06-17 01:34:17,435] [INFO] Selected 20 target genomes.
[2023-06-17 01:34:17,435] [INFO] Target genome list was writen to GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:34:17,478] [INFO] Task started: fastANI
[2023-06-17 01:34:17,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f121296-04aa-4655-92d0-18a01bd46616/GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna.gz --refList GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/target_genomes_gtdb.txt --output GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:34:28,374] [INFO] Task succeeded: fastANI
[2023-06-17 01:34:28,391] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:34:28,392] [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_004346095.1	s__Faecalimonas umbilicata	98.3676	725	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.30	97.78	0.83	0.78	20	conclusive
GCA_900546325.1	s__Faecalimonas sp900546325	87.5867	597	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	99.83	99.66	0.93	0.88	3	-
GCF_003435815.1	s__CAG-317 sp000433215	79.9551	139	839	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_902381685.1	s__Faecalimonas sp000209385	79.8656	136	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	99.49	98.98	0.93	0.86	3	-
GCF_900104635.1	s__Faecalimonas phoceensis	79.7108	169	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.10	95.01	0.81	0.60	21	-
GCA_900551895.1	s__Faecalimonas sp900551895	79.0019	110	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	98.69	98.58	0.83	0.80	3	-
GCF_018228665.1	s__UBA9414 sp003458885	78.8193	168	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	97.84	97.84	0.85	0.85	3	-
GCA_900550235.1	s__Faecalimonas sp900550235	78.5945	127	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	78.5401	129	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_000155875.1	s__Bariatricus comes	78.3133	120	839	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_001404875.1	s__Dorea_A longicatena_B	78.2373	119	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCA_018365895.1	s__UBA9414 sp018365895	77.9569	138	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA9414	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012524165.2	s__Muricomes sp012524165	77.7074	116	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Muricomes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433535.1	s__CAG-317 sp000433535	77.5578	117	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.49	98.19	0.84	0.83	3	-
GCA_910576335.1	s__UBA7109 sp910576335	77.1753	73	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	99.46	98.92	0.97	0.94	3	-
GCA_900550865.1	s__Dorea_A sp900550865	77.1401	92	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	76.955	60	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCA_016295505.1	s__Dorea_A sp016295505	76.8312	82	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419285.1	s__Mediterraneibacter caccogallinarum	76.4171	60	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.44	97.89	0.90	0.83	10	-
GCA_900556835.1	s__Faecalimonas sp900556835	76.0454	100	839	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Faecalimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:34:28,394] [INFO] GTDB search result was written to GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/result_gtdb.tsv
[2023-06-17 01:34:28,406] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:34:28,414] [INFO] DFAST_QC result json was written to GCA_905192565.1_ERR1430482-mag-bin.28_genomic.fna/dqc_result.json
[2023-06-17 01:34:28,414] [INFO] DFAST_QC completed!
[2023-06-17 01:34:28,414] [INFO] Total running time: 0h0m56s