[2023-06-14 01:25:48,599] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:25:48,605] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:25:48,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference
[2023-06-14 01:25:50,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:25:50,348] [INFO] Task started: Prodigal
[2023-06-14 01:25:50,348] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8d6bb54-fed0-403a-b1ad-ac69b52f9acf/GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:25:55,998] [INFO] Task succeeded: Prodigal
[2023-06-14 01:25:55,998] [INFO] Task started: HMMsearch
[2023-06-14 01:25:55,998] [INFO] Running command: hmmsearch --tblout GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference/reference_markers.hmm GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:25:56,215] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:25:56,217] [INFO] Found 6/6 markers.
[2023-06-14 01:25:56,250] [INFO] Query marker FASTA was written to GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-14 01:25:56,250] [INFO] Task started: Blastn
[2023-06-14 01:25:56,250] [INFO] Running command: blastn -query GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference/reference_markers.fasta -out GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:25:56,854] [INFO] Task succeeded: Blastn
[2023-06-14 01:25:56,857] [INFO] Selected 22 target genomes.
[2023-06-14 01:25:56,857] [INFO] Target genome list was writen to GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:25:56,859] [INFO] Task started: fastANI
[2023-06-14 01:25:56,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d6bb54-fed0-403a-b1ad-ac69b52f9acf/GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:26:08,036] [INFO] Task succeeded: fastANI
[2023-06-14 01:26:08,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:26:08,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:26:08,043] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:26:08,043] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-14 01:26:08,043] [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
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	79.6281	220	816	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	79.3921	219	816	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	79.0078	106	816	95	below_threshold
Lachnospira eligens	strain=ATCC 27750	GCA_000146185.1	39485	39485	suspected-type	True	77.5104	70	816	95	below_threshold
Eubacterium ruminantium	strain=ATCC 17233	GCA_900167085.1	42322	42322	type	True	77.4888	75	816	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	77.0484	50	816	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 01:26:08,045] [INFO] DFAST Taxonomy check result was written to GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:26:08,046] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:26:08,046] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:26:08,046] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference/checkm_data
[2023-06-14 01:26:08,047] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:26:08,073] [INFO] Task started: CheckM
[2023-06-14 01:26:08,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-14 01:26:30,571] [INFO] Task succeeded: CheckM
[2023-06-14 01:26:30,572] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:26:30,587] [INFO] ===== Completeness check finished =====
[2023-06-14 01:26:30,587] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:26:30,588] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:26:30,588] [INFO] Task started: Blastn
[2023-06-14 01:26:30,588] [INFO] Running command: blastn -query GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc18dfeb-bc41-4828-b7b7-46dddf6b6c03/dqc_reference/reference_markers_gtdb.fasta -out GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:26:31,554] [INFO] Task succeeded: Blastn
[2023-06-14 01:26:31,558] [INFO] Selected 24 target genomes.
[2023-06-14 01:26:31,558] [INFO] Target genome list was writen to GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:26:31,585] [INFO] Task started: fastANI
[2023-06-14 01:26:31,585] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8d6bb54-fed0-403a-b1ad-ac69b52f9acf/GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:26:41,050] [INFO] Task succeeded: fastANI
[2023-06-14 01:26:41,065] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:26:41,066] [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_003482105.1	s__Coprococcus sp000433075	98.0874	734	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	99.05	98.02	0.96	0.92	5	conclusive
GCF_001404675.1	s__Coprococcus eutactus_A	79.7704	229	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.33	97.53	0.90	0.82	34	-
GCF_000154245.1	s__Coprococcus sp000154245	79.7438	192	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.94	98.58	0.93	0.88	6	-
GCF_003461625.1	s__Coprococcus sp900066115	79.5422	193	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.16	97.77	0.91	0.89	23	-
GCF_000154425.1	s__Coprococcus eutactus	79.3707	220	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	98.55	98.02	0.90	0.86	8	-
GCA_900557435.1	s__Coprococcus sp900557435	78.8936	130	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548315.1	s__Coprococcus sp900548315	78.8674	157	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016297325.1	s__Coprococcus sp016297325	78.6592	166	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017935345.1	s__Coprococcus sp017935345	78.6548	143	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437435.1	s__Coprococcus sp002437435	78.3866	160	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296785.1	s__Coprococcus sp016296785	78.2837	144	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017624085.1	s__Coprococcus sp017624085	78.1175	75	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Coprococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287955.1	s__Lachnospira sp900316325	77.7376	62	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
GCA_017420535.1	s__Eubacterium_Q sp017420535	77.2213	72	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774725.1	s__Eubacterium_Q sp902774725	77.1211	58	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	96.31	95.93	0.76	0.75	3	-
GCA_017938485.1	s__CAG-127 sp017938485	77.1203	72	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800325.1	s__CAG-127 sp902800325	76.9516	75	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	98.34	96.92	0.85	0.82	5	-
GCA_002314775.1	s__UBA1760 sp002314775	76.414	74	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1760	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321215.1	s__Eubacterium_Q sp900321215	76.2625	60	816	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_Q	95.0	99.10	98.50	0.87	0.75	5	-
--------------------------------------------------------------------------------
[2023-06-14 01:26:41,068] [INFO] GTDB search result was written to GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:26:41,068] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:26:41,072] [INFO] DFAST_QC result json was written to GCA_938048665.1_SRR413754_bin.94_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:26:41,072] [INFO] DFAST_QC completed!
[2023-06-14 01:26:41,072] [INFO] Total running time: 0h0m52s