[2023-03-16 20:37:55,739] [INFO] DFAST_QC pipeline started.
[2023-03-16 20:37:55,739] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 20:37:55,739] [INFO] DQC Reference Directory: /var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference
[2023-03-16 20:37:57,592] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 20:37:57,592] [INFO] Task started: Prodigal
[2023-03-16 20:37:57,592] [INFO] Running command: cat /var/lib/cwl/stgc79c3f44-0c31-4486-9acf-995c11db337e/OceanDNA-b30236.fa | prodigal -d OceanDNA-b30236/cds.fna -a OceanDNA-b30236/protein.faa -g 11 -q > /dev/null
[2023-03-16 20:38:21,433] [INFO] Task succeeded: Prodigal
[2023-03-16 20:38:21,434] [INFO] Task started: HMMsearch
[2023-03-16 20:38:21,434] [INFO] Running command: hmmsearch --tblout OceanDNA-b30236/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference/reference_markers.hmm OceanDNA-b30236/protein.faa > /dev/null
[2023-03-16 20:38:21,678] [INFO] Task succeeded: HMMsearch
[2023-03-16 20:38:21,679] [INFO] Found 6/6 markers.
[2023-03-16 20:38:21,696] [INFO] Query marker FASTA was written to OceanDNA-b30236/markers.fasta
[2023-03-16 20:38:21,697] [INFO] Task started: Blastn
[2023-03-16 20:38:21,697] [INFO] Running command: blastn -query OceanDNA-b30236/markers.fasta -db /var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference/reference_markers.fasta -out OceanDNA-b30236/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:38:22,553] [INFO] Task succeeded: Blastn
[2023-03-16 20:38:22,554] [INFO] Selected 20 target genomes.
[2023-03-16 20:38:22,554] [INFO] Target genome list was writen to OceanDNA-b30236/target_genomes.txt
[2023-03-16 20:38:22,566] [INFO] Task started: fastANI
[2023-03-16 20:38:22,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgc79c3f44-0c31-4486-9acf-995c11db337e/OceanDNA-b30236.fa --refList OceanDNA-b30236/target_genomes.txt --output OceanDNA-b30236/fastani_result.tsv --threads 1
[2023-03-16 20:38:37,887] [INFO] Task succeeded: fastANI
[2023-03-16 20:38:37,887] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 20:38:37,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 20:38:37,899] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 20:38:37,899] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 20:38:37,899] [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 sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	79.031	435	769	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.5739	403	769	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.5379	356	769	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	78.5353	364	769	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.5314	410	769	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.4872	352	769	95	below_threshold
Allosediminivita pacifica	strain=CGMCC 1.12410	GCA_014637495.1	1267769	1267769	type	True	78.4705	291	769	95	below_threshold
Allosediminivita pacifica	strain=DSM 29329	GCA_003054175.1	1267769	1267769	type	True	78.463	289	769	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.2627	349	769	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	78.2625	346	769	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	78.2569	362	769	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.2158	337	769	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	78.2144	331	769	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.2101	341	769	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.9825	287	769	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	77.967	307	769	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.8535	314	769	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.7662	289	769	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.5111	273	769	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.4963	310	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 20:38:37,900] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30236/tc_result.tsv
[2023-03-16 20:38:37,900] [INFO] ===== Taxonomy check completed =====
[2023-03-16 20:38:37,900] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 20:38:37,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference/checkm_data
[2023-03-16 20:38:37,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 20:38:37,927] [INFO] Task started: CheckM
[2023-03-16 20:38:37,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30236/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30236/checkm_input OceanDNA-b30236/checkm_result
[2023-03-16 20:39:15,951] [INFO] Task succeeded: CheckM
[2023-03-16 20:39:15,951] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 20:39:15,954] [INFO] ===== Completeness check finished =====
[2023-03-16 20:39:15,954] [INFO] ===== Start GTDB Search =====
[2023-03-16 20:39:15,954] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30236/markers.fasta)
[2023-03-16 20:39:15,955] [INFO] Task started: Blastn
[2023-03-16 20:39:15,955] [INFO] Running command: blastn -query OceanDNA-b30236/markers.fasta -db /var/lib/cwl/stg20a7debc-71d2-4fcf-a3dc-362981e4af25/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30236/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 20:39:17,427] [INFO] Task succeeded: Blastn
[2023-03-16 20:39:17,429] [INFO] Selected 19 target genomes.
[2023-03-16 20:39:17,429] [INFO] Target genome list was writen to OceanDNA-b30236/target_genomes_gtdb.txt
[2023-03-16 20:39:17,455] [INFO] Task started: fastANI
[2023-03-16 20:39:17,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgc79c3f44-0c31-4486-9acf-995c11db337e/OceanDNA-b30236.fa --refList OceanDNA-b30236/target_genomes_gtdb.txt --output OceanDNA-b30236/fastani_result_gtdb.tsv --threads 1
[2023-03-16 20:39:34,659] [INFO] Task succeeded: fastANI
[2023-03-16 20:39:34,670] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 20:39:34,670] [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_001886735.1	s__Sulfitobacter alexandrii	80.197	496	769	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	79.9899	503	769	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	79.8796	491	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	79.4801	416	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_001650875.1	s__Sulfitobacter sp001650875	79.4304	473	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634885.1	s__Sulfitobacter sp001634885	79.226	383	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCF_003344785.1	s__Puniceibacterium profundi	79.0841	386	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003651245.1	s__Roseovarius spongiae	78.6255	335	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.5739	403	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_004358185.1	s__Antarcticimicrobium luteum	78.5233	365	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	78.511	392	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.4888	426	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.4427	355	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428585.1	s__Sedimentitalea sp016428585	78.4081	336	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	78.2627	349	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_900113435.1	s__Sulfitobacter dubius	78.2467	363	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_005938225.1	s__Arenibacterium halophilum	78.2031	337	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCF_013346665.1	s__Sulfitobacter maritimus	77.967	307	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014763045.1	s__Sulfitobacter aestuariivivens	77.7779	288	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 20:39:34,671] [INFO] GTDB search result was written to OceanDNA-b30236/result_gtdb.tsv
[2023-03-16 20:39:34,671] [INFO] ===== GTDB Search completed =====
[2023-03-16 20:39:34,676] [INFO] DFAST_QC result json was written to OceanDNA-b30236/dqc_result.json
[2023-03-16 20:39:34,676] [INFO] DFAST_QC completed!
[2023-03-16 20:39:34,676] [INFO] Total running time: 0h1m39s