[2024-01-24 14:14:19,912] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:19,915] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:19,915] [INFO] DQC Reference Directory: /var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference
[2024-01-24 14:14:21,273] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:21,274] [INFO] Task started: Prodigal
[2024-01-24 14:14:21,275] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7aa9986-2723-4bc0-a336-3f1541a6088c/GCF_014197555.1_ASM1419755v1_genomic.fna.gz | prodigal -d GCF_014197555.1_ASM1419755v1_genomic.fna/cds.fna -a GCF_014197555.1_ASM1419755v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:35,018] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:35,019] [INFO] Task started: HMMsearch
[2024-01-24 14:14:35,019] [INFO] Running command: hmmsearch --tblout GCF_014197555.1_ASM1419755v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference/reference_markers.hmm GCF_014197555.1_ASM1419755v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:35,319] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:35,320] [INFO] Found 6/6 markers.
[2024-01-24 14:14:35,357] [INFO] Query marker FASTA was written to GCF_014197555.1_ASM1419755v1_genomic.fna/markers.fasta
[2024-01-24 14:14:35,358] [INFO] Task started: Blastn
[2024-01-24 14:14:35,358] [INFO] Running command: blastn -query GCF_014197555.1_ASM1419755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference/reference_markers.fasta -out GCF_014197555.1_ASM1419755v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:36,102] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:36,106] [INFO] Selected 15 target genomes.
[2024-01-24 14:14:36,106] [INFO] Target genome list was writen to GCF_014197555.1_ASM1419755v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:36,115] [INFO] Task started: fastANI
[2024-01-24 14:14:36,115] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7aa9986-2723-4bc0-a336-3f1541a6088c/GCF_014197555.1_ASM1419755v1_genomic.fna.gz --refList GCF_014197555.1_ASM1419755v1_genomic.fna/target_genomes.txt --output GCF_014197555.1_ASM1419755v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:47,231] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:47,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:47,232] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:47,245] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:47,245] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:47,245] [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
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	100.0	1352	1353	95	conclusive
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	99.9977	1348	1353	95	conclusive
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	81.1616	646	1353	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	81.1039	656	1353	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	79.4512	592	1353	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	78.3813	519	1353	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.3251	424	1353	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	78.1714	305	1353	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.1601	369	1353	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.4526	373	1353	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.9192	130	1353	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.8532	139	1353	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.4781	133	1353	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.2053	89	1353	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.035	109	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:47,247] [INFO] DFAST Taxonomy check result was written to GCF_014197555.1_ASM1419755v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:47,247] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:47,248] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:47,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference/checkm_data
[2024-01-24 14:14:47,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:47,289] [INFO] Task started: CheckM
[2024-01-24 14:14:47,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197555.1_ASM1419755v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197555.1_ASM1419755v1_genomic.fna/checkm_input GCF_014197555.1_ASM1419755v1_genomic.fna/checkm_result
[2024-01-24 14:15:28,298] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:28,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:28,315] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:28,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:28,315] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197555.1_ASM1419755v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:28,316] [INFO] Task started: Blastn
[2024-01-24 14:15:28,316] [INFO] Running command: blastn -query GCF_014197555.1_ASM1419755v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgffea3b37-b3e5-4cd9-bb2d-d07d62850835/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197555.1_ASM1419755v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:29,452] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:29,456] [INFO] Selected 14 target genomes.
[2024-01-24 14:15:29,457] [INFO] Target genome list was writen to GCF_014197555.1_ASM1419755v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:29,471] [INFO] Task started: fastANI
[2024-01-24 14:15:29,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7aa9986-2723-4bc0-a336-3f1541a6088c/GCF_014197555.1_ASM1419755v1_genomic.fna.gz --refList GCF_014197555.1_ASM1419755v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197555.1_ASM1419755v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:40,372] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:40,385] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:40,385] [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_000622385.1	s__Sulfitobacter noctilucicola	99.9977	1348	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000622325.1	s__Sulfitobacter geojensis	81.1788	644	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_000622365.1	s__Sulfitobacter noctilucae	79.4595	592	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	78.6197	461	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.5519	538	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	78.3848	518	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.3416	494	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.3064	467	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	78.1714	305	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	78.0468	371	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_900102535.1	s__Sulfitobacter delicatus	77.9728	357	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.9697	414	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.717	377	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.5529	371	1353	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,387] [INFO] GTDB search result was written to GCF_014197555.1_ASM1419755v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:40,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:40,392] [INFO] DFAST_QC result json was written to GCF_014197555.1_ASM1419755v1_genomic.fna/dqc_result.json
[2024-01-24 14:15:40,392] [INFO] DFAST_QC completed!
[2024-01-24 14:15:40,392] [INFO] Total running time: 0h1m20s