[2023-06-05 07:09:37,547] [INFO] DFAST_QC pipeline started.
[2023-06-05 07:09:37,550] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 07:09:37,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference
[2023-06-05 07:09:39,669] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 07:09:39,670] [INFO] Task started: Prodigal
[2023-06-05 07:09:39,670] [INFO] Running command: gunzip -c /var/lib/cwl/stga1b23ccb-0656-4da9-902c-ea4c30fa1654/GCA_934754485.1_ERR7745594_bin.140_genomic.fna.gz | prodigal -d GCA_934754485.1_ERR7745594_bin.140_genomic.fna/cds.fna -a GCA_934754485.1_ERR7745594_bin.140_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 07:09:43,053] [INFO] Task succeeded: Prodigal
[2023-06-05 07:09:43,053] [INFO] Task started: HMMsearch
[2023-06-05 07:09:43,053] [INFO] Running command: hmmsearch --tblout GCA_934754485.1_ERR7745594_bin.140_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference/reference_markers.hmm GCA_934754485.1_ERR7745594_bin.140_genomic.fna/protein.faa > /dev/null
[2023-06-05 07:09:43,315] [INFO] Task succeeded: HMMsearch
[2023-06-05 07:09:43,316] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga1b23ccb-0656-4da9-902c-ea4c30fa1654/GCA_934754485.1_ERR7745594_bin.140_genomic.fna.gz]
[2023-06-05 07:09:43,342] [INFO] Query marker FASTA was written to GCA_934754485.1_ERR7745594_bin.140_genomic.fna/markers.fasta
[2023-06-05 07:09:43,343] [INFO] Task started: Blastn
[2023-06-05 07:09:43,343] [INFO] Running command: blastn -query GCA_934754485.1_ERR7745594_bin.140_genomic.fna/markers.fasta -db /var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference/reference_markers.fasta -out GCA_934754485.1_ERR7745594_bin.140_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:09:44,643] [INFO] Task succeeded: Blastn
[2023-06-05 07:09:44,647] [INFO] Selected 19 target genomes.
[2023-06-05 07:09:44,648] [INFO] Target genome list was writen to GCA_934754485.1_ERR7745594_bin.140_genomic.fna/target_genomes.txt
[2023-06-05 07:09:44,653] [INFO] Task started: fastANI
[2023-06-05 07:09:44,653] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b23ccb-0656-4da9-902c-ea4c30fa1654/GCA_934754485.1_ERR7745594_bin.140_genomic.fna.gz --refList GCA_934754485.1_ERR7745594_bin.140_genomic.fna/target_genomes.txt --output GCA_934754485.1_ERR7745594_bin.140_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 07:09:55,045] [INFO] Task succeeded: fastANI
[2023-06-05 07:09:55,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 07:09:55,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 07:09:55,063] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 07:09:55,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 07:09:55,064] [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
Clostridium saudiense	strain=JCC	GCA_000577815.1	1414720	1414720	type	True	79.3737	294	704	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	79.1742	282	704	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	77.9667	191	704	95	below_threshold
Clostridium septicum	strain=DSM 7534	GCA_003606265.1	1504	1504	type	True	77.9544	196	704	95	below_threshold
Clostridium septicum	strain=FDAARGOS_1551	GCA_020736665.1	1504	1504	type	True	77.94	195	704	95	below_threshold
Clostridium nigeriense	strain=Marseille-P2414	GCA_900086595.1	1805470	1805470	type	True	77.8293	198	704	95	below_threshold
Clostridium gallinarum	strain=Sa3CUN1	GCA_014836325.1	2762246	2762246	type	True	77.7369	193	704	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	77.645	129	704	95	below_threshold
Clostridium paraputrificum	strain=NCTC11833	GCA_900447045.1	29363	29363	type	True	77.6086	182	704	95	below_threshold
Clostridium moniliforme	strain=DSM 3984	GCA_017873235.1	39489	39489	type	True	77.4833	157	704	95	below_threshold
Clostridium weizhouense	strain=YB-6	GCA_019431045.1	2859781	2859781	type	True	77.1701	184	704	95	below_threshold
Clostridium cibarium	strain=Sa3CVN1	GCA_014836335.1	2762247	2762247	type	True	77.1341	134	704	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=ATCC 27021	GCA_000334435.1	36745	36745	type	True	76.7209	156	704	95	below_threshold
Clostridium manihotivorum	strain=CT4	GCA_004015185.1	2320868	2320868	type	True	76.5751	111	704	95	below_threshold
Clostridium saccharoperbutylacetonicum	strain=N1-4(HMT)	GCA_000340885.1	36745	36745	type	True	76.5437	162	704	95	below_threshold
Clostridium faecium	strain=N37	GCA_014836835.1	2762223	2762223	type	True	76.2883	93	704	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 07:09:55,066] [INFO] DFAST Taxonomy check result was written to GCA_934754485.1_ERR7745594_bin.140_genomic.fna/tc_result.tsv
[2023-06-05 07:09:55,066] [INFO] ===== Taxonomy check completed =====
[2023-06-05 07:09:55,067] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 07:09:55,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference/checkm_data
[2023-06-05 07:09:55,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 07:09:55,097] [INFO] Task started: CheckM
[2023-06-05 07:09:55,098] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934754485.1_ERR7745594_bin.140_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934754485.1_ERR7745594_bin.140_genomic.fna/checkm_input GCA_934754485.1_ERR7745594_bin.140_genomic.fna/checkm_result
[2023-06-05 07:10:12,729] [INFO] Task succeeded: CheckM
[2023-06-05 07:10:12,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 07:10:12,758] [INFO] ===== Completeness check finished =====
[2023-06-05 07:10:12,759] [INFO] ===== Start GTDB Search =====
[2023-06-05 07:10:12,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934754485.1_ERR7745594_bin.140_genomic.fna/markers.fasta)
[2023-06-05 07:10:12,760] [INFO] Task started: Blastn
[2023-06-05 07:10:12,760] [INFO] Running command: blastn -query GCA_934754485.1_ERR7745594_bin.140_genomic.fna/markers.fasta -db /var/lib/cwl/stg60babffa-aa2a-4ef1-bcbd-ad579b59b8cc/dqc_reference/reference_markers_gtdb.fasta -out GCA_934754485.1_ERR7745594_bin.140_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 07:10:13,491] [INFO] Task succeeded: Blastn
[2023-06-05 07:10:13,495] [INFO] Selected 13 target genomes.
[2023-06-05 07:10:13,496] [INFO] Target genome list was writen to GCA_934754485.1_ERR7745594_bin.140_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 07:10:13,505] [INFO] Task started: fastANI
[2023-06-05 07:10:13,505] [INFO] Running command: fastANI --query /var/lib/cwl/stga1b23ccb-0656-4da9-902c-ea4c30fa1654/GCA_934754485.1_ERR7745594_bin.140_genomic.fna.gz --refList GCA_934754485.1_ERR7745594_bin.140_genomic.fna/target_genomes_gtdb.txt --output GCA_934754485.1_ERR7745594_bin.140_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 07:10:21,001] [INFO] Task succeeded: fastANI
[2023-06-05 07:10:21,017] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 07:10:21,018] [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_000435835.1	s__Clostridium sp000435835	98.9891	659	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	conclusive
GCF_014287815.1	s__Clostridium sp001916075	92.7564	583	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.32	99.07	0.94	0.92	6	-
GCA_900547475.1	s__Clostridium sp900547475	79.5182	279	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCA_900766315.1	s__Clostridium sp900766315	79.4894	296	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577815.1	s__Clostridium saudiense	79.3897	293	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.39	99.24	0.89	0.87	14	-
GCF_004353185.1	s__Clostridium cuniculi	79.2156	304	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	97.75	97.60	0.86	0.82	5	-
GCF_000320405.1	s__Clostridium celatum	79.1872	282	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.74	99.48	0.95	0.91	3	-
GCA_900543325.1	s__Clostridium sp900543325	79.17	269	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588715.1	s__Clostridium sp910588715	78.7562	280	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002327185.1	s__Clostridium chauvoei	77.9485	192	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_015550425.1	s__Clostridium sp015550425	77.8763	217	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.01	99.01	0.93	0.93	2	-
GCA_018372875.1	s__Clostridium sp018372875	77.8026	165	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.91	98.91	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-05 07:10:21,020] [INFO] GTDB search result was written to GCA_934754485.1_ERR7745594_bin.140_genomic.fna/result_gtdb.tsv
[2023-06-05 07:10:21,021] [INFO] ===== GTDB Search completed =====
[2023-06-05 07:10:21,026] [INFO] DFAST_QC result json was written to GCA_934754485.1_ERR7745594_bin.140_genomic.fna/dqc_result.json
[2023-06-05 07:10:21,026] [INFO] DFAST_QC completed!
[2023-06-05 07:10:21,027] [INFO] Total running time: 0h0m43s