[2024-01-24 11:20:19,435] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:19,437] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:19,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference
[2024-01-24 11:20:20,611] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:20,611] [INFO] Task started: Prodigal
[2024-01-24 11:20:20,612] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eb5e871-445a-40a0-a3fb-fa37965c5fd3/GCF_002807665.1_ASM280766v1_genomic.fna.gz | prodigal -d GCF_002807665.1_ASM280766v1_genomic.fna/cds.fna -a GCF_002807665.1_ASM280766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:30,291] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:30,291] [INFO] Task started: HMMsearch
[2024-01-24 11:20:30,292] [INFO] Running command: hmmsearch --tblout GCF_002807665.1_ASM280766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference/reference_markers.hmm GCF_002807665.1_ASM280766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:30,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:30,649] [INFO] Found 6/6 markers.
[2024-01-24 11:20:30,682] [INFO] Query marker FASTA was written to GCF_002807665.1_ASM280766v1_genomic.fna/markers.fasta
[2024-01-24 11:20:30,682] [INFO] Task started: Blastn
[2024-01-24 11:20:30,682] [INFO] Running command: blastn -query GCF_002807665.1_ASM280766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference/reference_markers.fasta -out GCF_002807665.1_ASM280766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:31,382] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:31,386] [INFO] Selected 23 target genomes.
[2024-01-24 11:20:31,386] [INFO] Target genome list was writen to GCF_002807665.1_ASM280766v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:31,414] [INFO] Task started: fastANI
[2024-01-24 11:20:31,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb5e871-445a-40a0-a3fb-fa37965c5fd3/GCF_002807665.1_ASM280766v1_genomic.fna.gz --refList GCF_002807665.1_ASM280766v1_genomic.fna/target_genomes.txt --output GCF_002807665.1_ASM280766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:46,214] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:46,215] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:46,216] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:46,228] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:46,228] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:46,228] [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
Alteromonas facilis	strain=P0213	GCA_002807665.1	2048004	2048004	type	True	100.0	1296	1297	95	conclusive
Alteromonas flava	strain=P0211	GCA_002807685.1	2048003	2048003	type	True	79.507	332	1297	95	below_threshold
Alteromonas alba	strain=190	GCA_002993365.1	2079529	2079529	type	True	78.8687	112	1297	95	below_threshold
Salinimonas lutimaris	strain=DPSR-4	GCA_005222225.1	914153	914153	type	True	78.7082	78	1297	95	below_threshold
Alteromonas abrolhosensis	strain=PEL67E	GCA_001953635.1	1892904	1892904	type	True	78.5585	94	1297	95	below_threshold
Alteromonas gracilis	strain=9a2	GCA_002993325.1	1479524	1479524	type	True	78.5059	94	1297	95	below_threshold
Salinimonas iocasae	strain=KX18D6	GCA_006228385.1	2572577	2572577	type	True	78.4965	80	1297	95	below_threshold
Alteromonas macleodii	strain=ATCC 27126	GCA_000172635.2	28108	28108	type	True	78.1542	102	1297	95	below_threshold
Alteromonas lipolytica	strain=JW12	GCA_001758465.1	1856405	1856405	type	True	78.1331	95	1297	95	below_threshold
Alteromonas portus	strain=HB161718	GCA_005117025.1	2565549	2565549	type	True	78.0632	93	1297	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	77.6804	67	1297	95	below_threshold
Alteromonas lipolytica	strain=CGMCC 1.15735	GCA_014643555.1	1856405	1856405	type	True	77.6419	97	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:46,230] [INFO] DFAST Taxonomy check result was written to GCF_002807665.1_ASM280766v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:46,230] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:46,230] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:46,231] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference/checkm_data
[2024-01-24 11:20:46,232] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:46,269] [INFO] Task started: CheckM
[2024-01-24 11:20:46,270] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002807665.1_ASM280766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002807665.1_ASM280766v1_genomic.fna/checkm_input GCF_002807665.1_ASM280766v1_genomic.fna/checkm_result
[2024-01-24 11:21:20,471] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:20,472] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:20,494] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:20,495] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:20,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002807665.1_ASM280766v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:20,495] [INFO] Task started: Blastn
[2024-01-24 11:21:20,496] [INFO] Running command: blastn -query GCF_002807665.1_ASM280766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14aa85f5-2b19-4d0d-88fe-bf3662d2acf8/dqc_reference/reference_markers_gtdb.fasta -out GCF_002807665.1_ASM280766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:21,572] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:21,577] [INFO] Selected 22 target genomes.
[2024-01-24 11:21:21,578] [INFO] Target genome list was writen to GCF_002807665.1_ASM280766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:21,600] [INFO] Task started: fastANI
[2024-01-24 11:21:21,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb5e871-445a-40a0-a3fb-fa37965c5fd3/GCF_002807665.1_ASM280766v1_genomic.fna.gz --refList GCF_002807665.1_ASM280766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002807665.1_ASM280766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:36,966] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:36,982] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:36,982] [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_002807665.1	s__Alteromonas_E facilis	100.0	1296	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002807685.1	s__Alteromonas_E flava	79.507	332	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993365.1	s__Alteromonas alba	78.8687	112	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155775.1	s__Glaciecola sp000155775	78.8533	63	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222225.1	s__Alteromonas lutimaris	78.7082	78	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953635.1	s__Alteromonas abrolhosensis	78.5585	94	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.27	97.25	0.92	0.89	10	-
GCF_001885075.1	s__Alteromonas sp001885075	78.5135	95	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006228385.1	s__Alteromonas iocasae	78.4965	80	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811415.1	s__Alteromonas sp009811415	78.2513	87	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001758465.1	s__Alteromonas lipolytica	78.2117	95	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000172635.2	s__Alteromonas macleodii	78.1542	102	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.79	96.10	0.88	0.76	56	-
GCF_006494365.1	s__Alteromonas mangrovi	77.9471	96	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000808575.1	s__Alteromonas marina	77.8509	105	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.44	97.44	0.91	0.91	2	-
GCF_014270035.1	s__Neptunicella marina	77.774	65	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Neptunicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500915.1	s__Alteromonas hispanica	77.755	87	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	97.81	97.72	0.82	0.79	5	-
GCA_019249295.1	s__Alteromonas antoniana	77.4576	90	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836745.1	s__Glaciecola sp002836745	77.3673	68	1297	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Glaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:36,984] [INFO] GTDB search result was written to GCF_002807665.1_ASM280766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:36,984] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:36,988] [INFO] DFAST_QC result json was written to GCF_002807665.1_ASM280766v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:36,988] [INFO] DFAST_QC completed!
[2024-01-24 11:21:36,988] [INFO] Total running time: 0h1m18s