[2023-03-15 17:39:54,920] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:39:54,920] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:39:54,920] [INFO] DQC Reference Directory: /var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference
[2023-03-15 17:39:57,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:39:57,555] [INFO] Task started: Prodigal
[2023-03-15 17:39:57,555] [INFO] Running command: cat /var/lib/cwl/stg6e38559e-87e7-46b5-a8ef-77cc65123fe5/OceanDNA-b30852.fa | prodigal -d OceanDNA-b30852/cds.fna -a OceanDNA-b30852/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:40:14,251] [INFO] Task succeeded: Prodigal
[2023-03-15 17:40:14,251] [INFO] Task started: HMMsearch
[2023-03-15 17:40:14,251] [INFO] Running command: hmmsearch --tblout OceanDNA-b30852/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference/reference_markers.hmm OceanDNA-b30852/protein.faa > /dev/null
[2023-03-15 17:40:14,437] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:40:14,438] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6e38559e-87e7-46b5-a8ef-77cc65123fe5/OceanDNA-b30852.fa]
[2023-03-15 17:40:14,458] [INFO] Query marker FASTA was written to OceanDNA-b30852/markers.fasta
[2023-03-15 17:40:14,460] [INFO] Task started: Blastn
[2023-03-15 17:40:14,460] [INFO] Running command: blastn -query OceanDNA-b30852/markers.fasta -db /var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference/reference_markers.fasta -out OceanDNA-b30852/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:40:15,068] [INFO] Task succeeded: Blastn
[2023-03-15 17:40:15,069] [INFO] Selected 15 target genomes.
[2023-03-15 17:40:15,069] [INFO] Target genome list was writen to OceanDNA-b30852/target_genomes.txt
[2023-03-15 17:40:15,079] [INFO] Task started: fastANI
[2023-03-15 17:40:15,079] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e38559e-87e7-46b5-a8ef-77cc65123fe5/OceanDNA-b30852.fa --refList OceanDNA-b30852/target_genomes.txt --output OceanDNA-b30852/fastani_result.tsv --threads 1
[2023-03-15 17:40:24,813] [INFO] Task succeeded: fastANI
[2023-03-15 17:40:24,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:40:24,813] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:40:24,821] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:40:24,822] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:40:24,822] [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
Thalassospira lohafexi	strain=139Z-12	GCA_002844275.1	744227	744227	type	True	84.1158	686	833	95	below_threshold
Thalassospira lucentensis	strain=DSM 14000	GCA_000421265.1	168935	168935	type	True	84.0473	682	833	95	below_threshold
Thalassospira lucentensis	strain=MCCC 1A00383	GCA_003326595.1	168935	168935	type	True	83.983	678	833	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	81.4945	586	833	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	81.3753	580	833	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	81.3067	579	833	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	81.2846	574	833	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	81.1378	577	833	95	below_threshold
Thalassospira australica	strain=NP 3b2	GCA_000763295.1	1528106	1528106	type	True	81.0633	529	833	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:40:24,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30852/tc_result.tsv
[2023-03-15 17:40:24,822] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:40:24,822] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:40:24,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference/checkm_data
[2023-03-15 17:40:24,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:40:24,828] [INFO] Task started: CheckM
[2023-03-15 17:40:24,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30852/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30852/checkm_input OceanDNA-b30852/checkm_result
[2023-03-15 17:41:09,674] [INFO] Task succeeded: CheckM
[2023-03-15 17:41:09,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.09%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:41:09,677] [INFO] ===== Completeness check finished =====
[2023-03-15 17:41:09,677] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:41:09,677] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30852/markers.fasta)
[2023-03-15 17:41:09,679] [INFO] Task started: Blastn
[2023-03-15 17:41:09,679] [INFO] Running command: blastn -query OceanDNA-b30852/markers.fasta -db /var/lib/cwl/stg45c2b3dd-14e0-4c2c-9b67-c2eb4cfe1602/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30852/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:41:10,698] [INFO] Task succeeded: Blastn
[2023-03-15 17:41:10,699] [INFO] Selected 14 target genomes.
[2023-03-15 17:41:10,699] [INFO] Target genome list was writen to OceanDNA-b30852/target_genomes_gtdb.txt
[2023-03-15 17:41:10,898] [INFO] Task started: fastANI
[2023-03-15 17:41:10,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e38559e-87e7-46b5-a8ef-77cc65123fe5/OceanDNA-b30852.fa --refList OceanDNA-b30852/target_genomes_gtdb.txt --output OceanDNA-b30852/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:41:21,928] [INFO] Task succeeded: fastANI
[2023-03-15 17:41:21,937] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 17:41:21,937] [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_011806425.1	s__Thalassospira lucentensis_B	96.8071	819	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002844275.1	s__Thalassospira lohafexi	84.1131	686	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	N/A	N/A	N/A	N/A	1	-
GCF_000421265.1	s__Thalassospira lucentensis	84.0399	683	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.8797	97.14	96.17	0.92	0.88	5	-
GCF_002844235.1	s__Thalassospira povalilytica	81.5057	585	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
GCF_001662875.1	s__Thalassospira tepidiphila	81.2948	580	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	96.58	95.57	0.94	0.88	15	-
GCF_000300275.1	s__Thalassospira profundimaris	81.2846	574	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.4963	N/A	N/A	N/A	N/A	1	-
GCF_017922435.1	s__Thalassospira sp017922435	81.2381	582	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.2246	N/A	N/A	N/A	N/A	1	-
GCA_002709775.1	s__Thalassospira sp002709775	81.2364	533	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000948415.1	s__Thalassospira sp000948415	81.1599	559	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	81.1488	576	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003326795.1	s__Thalassospira profundimaris_C	81.1252	539	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003326675.1	s__Thalassospira profundimaris_D	81.0679	565	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763295.1	s__Thalassospira australica	81.0633	529	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806525.1	s__Thalassospira sp011806525	80.993	558	833	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 17:41:21,938] [INFO] GTDB search result was written to OceanDNA-b30852/result_gtdb.tsv
[2023-03-15 17:41:21,938] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:41:21,939] [INFO] DFAST_QC result json was written to OceanDNA-b30852/dqc_result.json
[2023-03-15 17:41:21,940] [INFO] DFAST_QC completed!
[2023-03-15 17:41:21,940] [INFO] Total running time: 0h1m27s