[2023-03-18 03:45:10,278] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:45:10,278] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:45:10,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference
[2023-03-18 03:45:12,143] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:45:12,144] [INFO] Task started: Prodigal
[2023-03-18 03:45:12,144] [INFO] Running command: cat /var/lib/cwl/stg106617b5-6d51-4368-8848-551096fe0c3c/OceanDNA-b37601.fa | prodigal -d OceanDNA-b37601/cds.fna -a OceanDNA-b37601/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:45:32,273] [INFO] Task succeeded: Prodigal
[2023-03-18 03:45:32,273] [INFO] Task started: HMMsearch
[2023-03-18 03:45:32,274] [INFO] Running command: hmmsearch --tblout OceanDNA-b37601/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference/reference_markers.hmm OceanDNA-b37601/protein.faa > /dev/null
[2023-03-18 03:45:32,554] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:45:32,555] [INFO] Found 6/6 markers.
[2023-03-18 03:45:32,576] [INFO] Query marker FASTA was written to OceanDNA-b37601/markers.fasta
[2023-03-18 03:45:32,576] [INFO] Task started: Blastn
[2023-03-18 03:45:32,576] [INFO] Running command: blastn -query OceanDNA-b37601/markers.fasta -db /var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference/reference_markers.fasta -out OceanDNA-b37601/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:45:33,203] [INFO] Task succeeded: Blastn
[2023-03-18 03:45:33,204] [INFO] Selected 26 target genomes.
[2023-03-18 03:45:33,204] [INFO] Target genome list was writen to OceanDNA-b37601/target_genomes.txt
[2023-03-18 03:45:33,214] [INFO] Task started: fastANI
[2023-03-18 03:45:33,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg106617b5-6d51-4368-8848-551096fe0c3c/OceanDNA-b37601.fa --refList OceanDNA-b37601/target_genomes.txt --output OceanDNA-b37601/fastani_result.tsv --threads 1
[2023-03-18 03:45:50,929] [INFO] Task succeeded: fastANI
[2023-03-18 03:45:50,929] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:45:50,929] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:45:50,937] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:45:50,937] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:45:50,938] [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
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.7602	82	1080	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	76.6374	97	1080	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	76.462	110	1080	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.4183	115	1080	95	below_threshold
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	76.3881	81	1080	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.3813	86	1080	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.3782	85	1080	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.3568	86	1080	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	76.3244	86	1080	95	below_threshold
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	76.2275	80	1080	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	76.1908	107	1080	95	below_threshold
Halioglobus pacificus	strain=KCTC 23430	GCA_014652275.1	930806	930806	type	True	75.9891	69	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:45:50,938] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37601/tc_result.tsv
[2023-03-18 03:45:50,938] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:45:50,938] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:45:50,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference/checkm_data
[2023-03-18 03:45:50,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:45:50,985] [INFO] Task started: CheckM
[2023-03-18 03:45:50,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37601/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37601/checkm_input OceanDNA-b37601/checkm_result
[2023-03-18 03:46:41,549] [INFO] Task succeeded: CheckM
[2023-03-18 03:46:41,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:46:41,552] [INFO] ===== Completeness check finished =====
[2023-03-18 03:46:41,552] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:46:41,552] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37601/markers.fasta)
[2023-03-18 03:46:41,553] [INFO] Task started: Blastn
[2023-03-18 03:46:41,553] [INFO] Running command: blastn -query OceanDNA-b37601/markers.fasta -db /var/lib/cwl/stg8993eae0-0f79-47e6-88d8-2fc42c8350c8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37601/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:46:42,591] [INFO] Task succeeded: Blastn
[2023-03-18 03:46:42,592] [INFO] Selected 18 target genomes.
[2023-03-18 03:46:42,592] [INFO] Target genome list was writen to OceanDNA-b37601/target_genomes_gtdb.txt
[2023-03-18 03:46:42,630] [INFO] Task started: fastANI
[2023-03-18 03:46:42,631] [INFO] Running command: fastANI --query /var/lib/cwl/stg106617b5-6d51-4368-8848-551096fe0c3c/OceanDNA-b37601.fa --refList OceanDNA-b37601/target_genomes_gtdb.txt --output OceanDNA-b37601/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:46:54,948] [INFO] Task succeeded: fastANI
[2023-03-18 03:46:54,957] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:46:54,957] [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_902705825.1	s__Halioglobus japonicus_A	78.7202	514	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704305.1	s__Halioglobus sp016704305	78.3934	442	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.09	98.09	0.89	0.89	2	-
GCA_002699145.1	s__Halioglobus sp002699145	76.8927	146	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_003646405.1	s__Halioglobus sp003646405	76.7886	107	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	76.6374	97	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	76.5189	116	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	76.4435	111	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.3813	86	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCA_002862985.1	s__Halioglobus sp002862985	76.3266	132	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003719295.1	s__Haliea alexandrii	76.2275	80	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692965.1	s__NZNC01 sp002692965	76.2089	72	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCA_004354085.1	s__Halioglobus sp004354085	76.1854	106	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480565.1	s__Halioglobus sp905480565	76.1738	55	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	76.1049	96	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652275.1	s__Halioglobus_A pacificus	75.9891	69	1080	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus_A	95.0	98.67	98.67	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 03:46:54,958] [INFO] GTDB search result was written to OceanDNA-b37601/result_gtdb.tsv
[2023-03-18 03:46:54,958] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:46:54,960] [INFO] DFAST_QC result json was written to OceanDNA-b37601/dqc_result.json
[2023-03-18 03:46:54,960] [INFO] DFAST_QC completed!
[2023-03-18 03:46:54,960] [INFO] Total running time: 0h1m45s