[2024-01-25 17:37:35,494] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:35,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:35,495] [INFO] DQC Reference Directory: /var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference
[2024-01-25 17:37:36,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:36,615] [INFO] Task started: Prodigal
[2024-01-25 17:37:36,615] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b267332-3b1f-40fe-a92b-df5cec009fe7/GCF_016412875.1_ASM1641287v1_genomic.fna.gz | prodigal -d GCF_016412875.1_ASM1641287v1_genomic.fna/cds.fna -a GCF_016412875.1_ASM1641287v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:46,309] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:46,310] [INFO] Task started: HMMsearch
[2024-01-25 17:37:46,310] [INFO] Running command: hmmsearch --tblout GCF_016412875.1_ASM1641287v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference/reference_markers.hmm GCF_016412875.1_ASM1641287v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:46,536] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:46,537] [INFO] Found 6/6 markers.
[2024-01-25 17:37:46,569] [INFO] Query marker FASTA was written to GCF_016412875.1_ASM1641287v1_genomic.fna/markers.fasta
[2024-01-25 17:37:46,569] [INFO] Task started: Blastn
[2024-01-25 17:37:46,569] [INFO] Running command: blastn -query GCF_016412875.1_ASM1641287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference/reference_markers.fasta -out GCF_016412875.1_ASM1641287v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:47,534] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:47,537] [INFO] Selected 15 target genomes.
[2024-01-25 17:37:47,537] [INFO] Target genome list was writen to GCF_016412875.1_ASM1641287v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:47,542] [INFO] Task started: fastANI
[2024-01-25 17:37:47,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b267332-3b1f-40fe-a92b-df5cec009fe7/GCF_016412875.1_ASM1641287v1_genomic.fna.gz --refList GCF_016412875.1_ASM1641287v1_genomic.fna/target_genomes.txt --output GCF_016412875.1_ASM1641287v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:37:59,124] [INFO] Task succeeded: fastANI
[2024-01-25 17:37:59,125] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:37:59,125] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:37:59,136] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:37:59,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:37:59,136] [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
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	83.0614	788	1218	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	82.863	793	1218	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	79.6286	492	1218	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.5665	568	1218	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	79.5482	503	1218	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	79.5394	520	1218	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	78.9649	492	1218	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.847	424	1218	95	below_threshold
Limimaricola hongkongensis	strain=UST950701-009P	GCA_000365005.1	278132	278132	type	True	78.8035	448	1218	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.5933	424	1218	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.5842	452	1218	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	78.5452	390	1218	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	78.4847	398	1218	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.0325	402	1218	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.6444	337	1218	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:37:59,140] [INFO] DFAST Taxonomy check result was written to GCF_016412875.1_ASM1641287v1_genomic.fna/tc_result.tsv
[2024-01-25 17:37:59,141] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:37:59,141] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:37:59,141] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference/checkm_data
[2024-01-25 17:37:59,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:37:59,196] [INFO] Task started: CheckM
[2024-01-25 17:37:59,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016412875.1_ASM1641287v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016412875.1_ASM1641287v1_genomic.fna/checkm_input GCF_016412875.1_ASM1641287v1_genomic.fna/checkm_result
[2024-01-25 17:38:33,325] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:33,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:33,350] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:33,350] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:33,351] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016412875.1_ASM1641287v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:33,351] [INFO] Task started: Blastn
[2024-01-25 17:38:33,351] [INFO] Running command: blastn -query GCF_016412875.1_ASM1641287v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd50d4fed-e8c2-4e94-9434-45afc897a470/dqc_reference/reference_markers_gtdb.fasta -out GCF_016412875.1_ASM1641287v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:35,314] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:35,317] [INFO] Selected 14 target genomes.
[2024-01-25 17:38:35,317] [INFO] Target genome list was writen to GCF_016412875.1_ASM1641287v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:35,323] [INFO] Task started: fastANI
[2024-01-25 17:38:35,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b267332-3b1f-40fe-a92b-df5cec009fe7/GCF_016412875.1_ASM1641287v1_genomic.fna.gz --refList GCF_016412875.1_ASM1641287v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016412875.1_ASM1641287v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:46,519] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:46,528] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:46,529] [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_016412875.1	s__Palleronia pontilimi	100.0	1217	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900141995.1	s__Palleronia salina	83.0421	786	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	82.85	794	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	79.5808	567	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	79.5725	499	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002869745.1	s__Oceaniglobus roseus	79.457	601	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299575.1	s__Palleronia guishaninsula	79.4462	477	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302445.1	s__Palleronia abyssalis	79.1529	518	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	79.1528	553	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363795.1	s__Palleronia sp900609015	79.0906	495	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.8927	482	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009835145.1	s__Profundibacterium mesophilum	78.8525	455	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.5976	450	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.4261	415	1218	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:46,530] [INFO] GTDB search result was written to GCF_016412875.1_ASM1641287v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:46,531] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:46,534] [INFO] DFAST_QC result json was written to GCF_016412875.1_ASM1641287v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:46,534] [INFO] DFAST_QC completed!
[2024-01-25 17:38:46,534] [INFO] Total running time: 0h1m11s