[2024-01-24 13:41:25,833] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,835] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,835] [INFO] DQC Reference Directory: /var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference
[2024-01-24 13:41:27,148] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,149] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,149] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c2846e7-3df9-49cb-842d-6ee9e5217878/GCF_002869505.1_ASM286950v1_genomic.fna.gz | prodigal -d GCF_002869505.1_ASM286950v1_genomic.fna/cds.fna -a GCF_002869505.1_ASM286950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:39,894] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:39,895] [INFO] Task started: HMMsearch
[2024-01-24 13:41:39,895] [INFO] Running command: hmmsearch --tblout GCF_002869505.1_ASM286950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference/reference_markers.hmm GCF_002869505.1_ASM286950v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:40,251] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:40,253] [INFO] Found 6/6 markers.
[2024-01-24 13:41:40,296] [INFO] Query marker FASTA was written to GCF_002869505.1_ASM286950v1_genomic.fna/markers.fasta
[2024-01-24 13:41:40,296] [INFO] Task started: Blastn
[2024-01-24 13:41:40,296] [INFO] Running command: blastn -query GCF_002869505.1_ASM286950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference/reference_markers.fasta -out GCF_002869505.1_ASM286950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:41,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:41,251] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:41,251] [INFO] Target genome list was writen to GCF_002869505.1_ASM286950v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:41,256] [INFO] Task started: fastANI
[2024-01-24 13:41:41,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c2846e7-3df9-49cb-842d-6ee9e5217878/GCF_002869505.1_ASM286950v1_genomic.fna.gz --refList GCF_002869505.1_ASM286950v1_genomic.fna/target_genomes.txt --output GCF_002869505.1_ASM286950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,905] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,916] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:50,916] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,916] [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
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	100.0	1345	1345	95	conclusive
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	99.9948	1342	1345	95	conclusive
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	99.9894	1345	1345	95	conclusive
Halioglobus maricola	strain=IMCC14385	GCA_009388985.1	2601894	2601894	type	True	79.4067	548	1345	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.5526	382	1345	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.3941	350	1345	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.9201	287	1345	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.565	269	1345	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.6212	90	1345	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	76.5013	82	1345	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	76.4842	71	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,918] [INFO] DFAST Taxonomy check result was written to GCF_002869505.1_ASM286950v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,918] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,918] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference/checkm_data
[2024-01-24 13:41:50,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,961] [INFO] Task started: CheckM
[2024-01-24 13:41:50,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002869505.1_ASM286950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002869505.1_ASM286950v1_genomic.fna/checkm_input GCF_002869505.1_ASM286950v1_genomic.fna/checkm_result
[2024-01-24 13:42:30,683] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:30,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:30,707] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:30,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:30,708] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002869505.1_ASM286950v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:30,708] [INFO] Task started: Blastn
[2024-01-24 13:42:30,708] [INFO] Running command: blastn -query GCF_002869505.1_ASM286950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8492eb5-5988-4e3b-873f-a957224ee1f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002869505.1_ASM286950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:32,088] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:32,093] [INFO] Selected 13 target genomes.
[2024-01-24 13:42:32,093] [INFO] Target genome list was writen to GCF_002869505.1_ASM286950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:32,137] [INFO] Task started: fastANI
[2024-01-24 13:42:32,137] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c2846e7-3df9-49cb-842d-6ee9e5217878/GCF_002869505.1_ASM286950v1_genomic.fna.gz --refList GCF_002869505.1_ASM286950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002869505.1_ASM286950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:42,071] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:42,087] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:42,087] [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_001983995.1	s__Halioglobus japonicus	99.9894	1345	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	conclusive
GCF_009388985.1	s__Halioglobus maricola	79.4067	548	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	78.5526	382	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	78.3941	350	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	77.9993	307	1345	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	77.9124	287	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	77.7778	278	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.7692	302	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.7534	276	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.565	269	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002866825.1	s__Halioglobus lutimaris	77.54	245	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	98.98	98.98	0.91	0.91	2	-
GCA_002699145.1	s__Halioglobus sp002699145	77.2164	254	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002416125.1	s__Haliea sp002416125	76.9685	164	1345	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:42,089] [INFO] GTDB search result was written to GCF_002869505.1_ASM286950v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:42,090] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:42,096] [INFO] DFAST_QC result json was written to GCF_002869505.1_ASM286950v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:42,096] [INFO] DFAST_QC completed!
[2024-01-24 13:42:42,096] [INFO] Total running time: 0h1m16s