[2024-01-24 13:32:40,835] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:40,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:40,838] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference
[2024-01-24 13:32:42,202] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:42,203] [INFO] Task started: Prodigal
[2024-01-24 13:32:42,203] [INFO] Running command: gunzip -c /var/lib/cwl/stg2de42919-1aa1-45a2-805c-8c134f87a8c4/GCF_003259905.1_ASM325990v1_genomic.fna.gz | prodigal -d GCF_003259905.1_ASM325990v1_genomic.fna/cds.fna -a GCF_003259905.1_ASM325990v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:56,534] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:56,535] [INFO] Task started: HMMsearch
[2024-01-24 13:32:56,535] [INFO] Running command: hmmsearch --tblout GCF_003259905.1_ASM325990v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference/reference_markers.hmm GCF_003259905.1_ASM325990v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:56,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:56,824] [INFO] Found 6/6 markers.
[2024-01-24 13:32:56,875] [INFO] Query marker FASTA was written to GCF_003259905.1_ASM325990v1_genomic.fna/markers.fasta
[2024-01-24 13:32:56,876] [INFO] Task started: Blastn
[2024-01-24 13:32:56,876] [INFO] Running command: blastn -query GCF_003259905.1_ASM325990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference/reference_markers.fasta -out GCF_003259905.1_ASM325990v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:57,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:57,886] [INFO] Selected 13 target genomes.
[2024-01-24 13:32:57,887] [INFO] Target genome list was writen to GCF_003259905.1_ASM325990v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:57,905] [INFO] Task started: fastANI
[2024-01-24 13:32:57,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg2de42919-1aa1-45a2-805c-8c134f87a8c4/GCF_003259905.1_ASM325990v1_genomic.fna.gz --refList GCF_003259905.1_ASM325990v1_genomic.fna/target_genomes.txt --output GCF_003259905.1_ASM325990v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:12,191] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:12,191] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:12,192] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:12,206] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:12,206] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:12,207] [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
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	100.0	1481	1484	95	conclusive
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	99.9314	1414	1484	95	conclusive
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	81.232	858	1484	95	below_threshold
Salipiger bermudensis	strain=HTCC2601	GCA_000153725.1	344736	344736	type	True	80.2359	791	1484	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	80.0742	764	1484	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	80.0709	740	1484	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	80.0267	777	1484	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	79.9514	695	1484	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.9245	633	1484	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	78.9097	635	1484	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.9529	385	1484	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.5749	356	1484	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.7793	254	1484	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:12,208] [INFO] DFAST Taxonomy check result was written to GCF_003259905.1_ASM325990v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:12,209] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:12,209] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:12,209] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference/checkm_data
[2024-01-24 13:33:12,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:12,255] [INFO] Task started: CheckM
[2024-01-24 13:33:12,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003259905.1_ASM325990v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003259905.1_ASM325990v1_genomic.fna/checkm_input GCF_003259905.1_ASM325990v1_genomic.fna/checkm_result
[2024-01-24 13:33:58,442] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:58,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:58,463] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:58,463] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:58,464] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003259905.1_ASM325990v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:58,464] [INFO] Task started: Blastn
[2024-01-24 13:33:58,464] [INFO] Running command: blastn -query GCF_003259905.1_ASM325990v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9be23b8-dc57-4562-acab-ad060ef3248c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003259905.1_ASM325990v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:00,132] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:00,136] [INFO] Selected 11 target genomes.
[2024-01-24 13:34:00,136] [INFO] Target genome list was writen to GCF_003259905.1_ASM325990v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:00,153] [INFO] Task started: fastANI
[2024-01-24 13:34:00,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg2de42919-1aa1-45a2-805c-8c134f87a8c4/GCF_003259905.1_ASM325990v1_genomic.fna.gz --refList GCF_003259905.1_ASM325990v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003259905.1_ASM325990v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:11,676] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:11,693] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:11,693] [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_003259905.1	s__Salipiger aestuarii	100.0	1482	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.58	99.38	0.94	0.92	5	conclusive
GCF_018860705.1	s__Salipiger sp018860705	83.4554	978	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102075.1	s__Salipiger thiooxidans	81.2333	857	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.34	95.88	0.90	0.85	6	-
GCF_001975705.1	s__Salipiger abyssi	80.5348	800	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	80.4277	765	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153725.1	s__Salipiger bermudensis	80.2493	788	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	98.06	97.75	0.87	0.75	4	-
GCF_014643635.1	s__Salipiger pallidus	79.92	699	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001687105.1	s__Salipiger sp001687105	79.1366	648	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	96.47	96.47	0.82	0.82	2	-
GCF_003111685.1	s__Salipiger pacificus_A	78.9575	602	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	97.69	97.64	0.90	0.89	3	-
GCF_900116195.1	s__Salipiger pacificus	78.9175	635	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017255395.1	s__AWRV01 sp017255395	78.8898	585	1484	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:11,694] [INFO] GTDB search result was written to GCF_003259905.1_ASM325990v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:11,695] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:11,698] [INFO] DFAST_QC result json was written to GCF_003259905.1_ASM325990v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:11,698] [INFO] DFAST_QC completed!
[2024-01-24 13:34:11,698] [INFO] Total running time: 0h1m31s