[2023-03-18 23:11:07,039] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:11:07,039] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:11:07,040] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference
[2023-03-18 23:11:08,309] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:11:08,309] [INFO] Task started: Prodigal
[2023-03-18 23:11:08,309] [INFO] Running command: cat /var/lib/cwl/stg5af5b6dc-b989-466e-82cc-cacbc291428b/OceanDNA-b30257.fa | prodigal -d OceanDNA-b30257/cds.fna -a OceanDNA-b30257/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:11:27,542] [INFO] Task succeeded: Prodigal
[2023-03-18 23:11:27,542] [INFO] Task started: HMMsearch
[2023-03-18 23:11:27,542] [INFO] Running command: hmmsearch --tblout OceanDNA-b30257/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference/reference_markers.hmm OceanDNA-b30257/protein.faa > /dev/null
[2023-03-18 23:11:27,854] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:11:27,855] [INFO] Found 6/6 markers.
[2023-03-18 23:11:27,881] [INFO] Query marker FASTA was written to OceanDNA-b30257/markers.fasta
[2023-03-18 23:11:27,881] [INFO] Task started: Blastn
[2023-03-18 23:11:27,881] [INFO] Running command: blastn -query OceanDNA-b30257/markers.fasta -db /var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference/reference_markers.fasta -out OceanDNA-b30257/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:11:28,616] [INFO] Task succeeded: Blastn
[2023-03-18 23:11:28,617] [INFO] Selected 20 target genomes.
[2023-03-18 23:11:28,617] [INFO] Target genome list was writen to OceanDNA-b30257/target_genomes.txt
[2023-03-18 23:11:28,634] [INFO] Task started: fastANI
[2023-03-18 23:11:28,634] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af5b6dc-b989-466e-82cc-cacbc291428b/OceanDNA-b30257.fa --refList OceanDNA-b30257/target_genomes.txt --output OceanDNA-b30257/fastani_result.tsv --threads 1
[2023-03-18 23:11:44,443] [INFO] Task succeeded: fastANI
[2023-03-18 23:11:44,443] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:11:44,443] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:11:44,453] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 23:11:44,453] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 23:11:44,453] [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 litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	98.9296	919	980	95	conclusive
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	88.0282	852	980	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	79.762	519	980	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.9049	397	980	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.8438	409	980	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.646	403	980	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.6322	408	980	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	78.1261	369	980	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.0777	366	980	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.9295	378	980	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.6983	333	980	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.5699	295	980	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	77.2215	214	980	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	76.8371	229	980	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	76.6833	195	980	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	76.5526	122	980	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	76.4241	124	980	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:11:44,454] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30257/tc_result.tsv
[2023-03-18 23:11:44,454] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:11:44,454] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:11:44,454] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference/checkm_data
[2023-03-18 23:11:44,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:11:44,471] [INFO] Task started: CheckM
[2023-03-18 23:11:44,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30257/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30257/checkm_input OceanDNA-b30257/checkm_result
[2023-03-18 23:12:33,296] [INFO] Task succeeded: CheckM
[2023-03-18 23:12:33,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:12:33,299] [INFO] ===== Completeness check finished =====
[2023-03-18 23:12:33,299] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:12:33,299] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30257/markers.fasta)
[2023-03-18 23:12:33,299] [INFO] Task started: Blastn
[2023-03-18 23:12:33,300] [INFO] Running command: blastn -query OceanDNA-b30257/markers.fasta -db /var/lib/cwl/stg7d5f5502-3087-4cf4-81ef-212e54e8d466/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30257/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:12:34,577] [INFO] Task succeeded: Blastn
[2023-03-18 23:12:34,578] [INFO] Selected 11 target genomes.
[2023-03-18 23:12:34,578] [INFO] Target genome list was writen to OceanDNA-b30257/target_genomes_gtdb.txt
[2023-03-18 23:12:34,589] [INFO] Task started: fastANI
[2023-03-18 23:12:34,589] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af5b6dc-b989-466e-82cc-cacbc291428b/OceanDNA-b30257.fa --refList OceanDNA-b30257/target_genomes_gtdb.txt --output OceanDNA-b30257/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:12:43,204] [INFO] Task succeeded: fastANI
[2023-03-18 23:12:43,211] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-18 23:12:43,211] [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_900103185.1	s__Sulfitobacter litoralis	98.9296	919	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	inconclusive
GCF_006064855.1	s__Sulfitobacter sp006064855	95.0527	832	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_900106935.1	s__Sulfitobacter pontiacus	88.0282	852	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_013282155.1	s__Sulfitobacter sp013282155	80.6814	581	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	80.3076	579	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	80.1792	469	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	79.752	520	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.2352	403	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.0577	368	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.5655	334	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	76.8368	229	980	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:12:43,211] [INFO] GTDB search result was written to OceanDNA-b30257/result_gtdb.tsv
[2023-03-18 23:12:43,211] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:12:43,213] [INFO] DFAST_QC result json was written to OceanDNA-b30257/dqc_result.json
[2023-03-18 23:12:43,213] [INFO] DFAST_QC completed!
[2023-03-18 23:12:43,213] [INFO] Total running time: 0h1m36s