[2023-03-15 13:03:53,436] [INFO] DFAST_QC pipeline started.
[2023-03-15 13:03:53,436] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 13:03:53,436] [INFO] DQC Reference Directory: /var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference
[2023-03-15 13:03:54,599] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 13:03:54,599] [INFO] Task started: Prodigal
[2023-03-15 13:03:54,599] [INFO] Running command: cat /var/lib/cwl/stg90399fe3-38b1-4f17-8669-acc5d7275a59/OceanDNA-b29592.fa | prodigal -d OceanDNA-b29592/cds.fna -a OceanDNA-b29592/protein.faa -g 11 -q > /dev/null
[2023-03-15 13:04:05,564] [INFO] Task succeeded: Prodigal
[2023-03-15 13:04:05,565] [INFO] Task started: HMMsearch
[2023-03-15 13:04:05,565] [INFO] Running command: hmmsearch --tblout OceanDNA-b29592/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference/reference_markers.hmm OceanDNA-b29592/protein.faa > /dev/null
[2023-03-15 13:04:05,775] [INFO] Task succeeded: HMMsearch
[2023-03-15 13:04:05,775] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg90399fe3-38b1-4f17-8669-acc5d7275a59/OceanDNA-b29592.fa]
[2023-03-15 13:04:05,793] [INFO] Query marker FASTA was written to OceanDNA-b29592/markers.fasta
[2023-03-15 13:04:05,793] [INFO] Task started: Blastn
[2023-03-15 13:04:05,793] [INFO] Running command: blastn -query OceanDNA-b29592/markers.fasta -db /var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference/reference_markers.fasta -out OceanDNA-b29592/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:06,580] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:06,580] [INFO] Selected 16 target genomes.
[2023-03-15 13:04:06,581] [INFO] Target genome list was writen to OceanDNA-b29592/target_genomes.txt
[2023-03-15 13:04:06,638] [INFO] Task started: fastANI
[2023-03-15 13:04:06,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg90399fe3-38b1-4f17-8669-acc5d7275a59/OceanDNA-b29592.fa --refList OceanDNA-b29592/target_genomes.txt --output OceanDNA-b29592/fastani_result.tsv --threads 1
[2023-03-15 13:04:16,656] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:16,656] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 13:04:16,657] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 13:04:16,668] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 13:04:16,668] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 13:04:16,668] [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
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	97.636	530	538	95	conclusive
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.1099	305	538	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.0126	290	538	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	78.952	278	538	95	below_threshold
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	78.9234	281	538	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.7828	259	538	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	77.8717	193	538	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	77.8643	235	538	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	77.8612	183	538	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.7695	179	538	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.5944	183	538	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.5774	213	538	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.5752	196	538	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	77.5446	198	538	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	77.4754	170	538	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.4058	143	538	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 13:04:16,668] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29592/tc_result.tsv
[2023-03-15 13:04:16,668] [INFO] ===== Taxonomy check completed =====
[2023-03-15 13:04:16,668] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 13:04:16,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference/checkm_data
[2023-03-15 13:04:16,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 13:04:16,677] [INFO] Task started: CheckM
[2023-03-15 13:04:16,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29592/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29592/checkm_input OceanDNA-b29592/checkm_result
[2023-03-15 13:04:47,771] [INFO] Task succeeded: CheckM
[2023-03-15 13:04:47,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 13:04:47,774] [INFO] ===== Completeness check finished =====
[2023-03-15 13:04:47,774] [INFO] ===== Start GTDB Search =====
[2023-03-15 13:04:47,774] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29592/markers.fasta)
[2023-03-15 13:04:47,775] [INFO] Task started: Blastn
[2023-03-15 13:04:47,775] [INFO] Running command: blastn -query OceanDNA-b29592/markers.fasta -db /var/lib/cwl/stg113b632e-c240-42d5-bce3-367891263a46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29592/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 13:04:49,092] [INFO] Task succeeded: Blastn
[2023-03-15 13:04:49,093] [INFO] Selected 17 target genomes.
[2023-03-15 13:04:49,093] [INFO] Target genome list was writen to OceanDNA-b29592/target_genomes_gtdb.txt
[2023-03-15 13:04:49,128] [INFO] Task started: fastANI
[2023-03-15 13:04:49,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg90399fe3-38b1-4f17-8669-acc5d7275a59/OceanDNA-b29592.fa --refList OceanDNA-b29592/target_genomes_gtdb.txt --output OceanDNA-b29592/fastani_result_gtdb.tsv --threads 1
[2023-03-15 13:04:59,792] [INFO] Task succeeded: fastANI
[2023-03-15 13:04:59,802] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 13:04:59,803] [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_000743715.1	s__Palleronia rufa	97.636	530	538	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_016412875.1	s__Palleronia pontilimi	79.3183	277	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	79.0919	305	538	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	78.9968	291	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_900172315.1	s__Palleronia marisminoris	78.9234	281	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004358695.1	s__Palleronia sp004358695	78.7901	258	538	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	78.7357	273	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363795.1	s__Palleronia sp900609015	78.4005	254	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004005435.1	s__CCMM004 sp004005435	78.2568	251	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.1488	262	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.0933	218	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009835145.1	s__Profundibacterium mesophilum	77.9522	190	538	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	77.8717	193	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004065.1	s__Palleronia caenipelagi	77.7695	179	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723615.1	s__Limimaricola cinnabarinus_B	77.7605	209	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689685.1	s__HKCCE3408 sp015689685	77.1193	207	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003075.1	s__IMCC34051 sp013003075	76.8391	111	538	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__IMCC34051	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 13:04:59,803] [INFO] GTDB search result was written to OceanDNA-b29592/result_gtdb.tsv
[2023-03-15 13:04:59,803] [INFO] ===== GTDB Search completed =====
[2023-03-15 13:04:59,805] [INFO] DFAST_QC result json was written to OceanDNA-b29592/dqc_result.json
[2023-03-15 13:04:59,805] [INFO] DFAST_QC completed!
[2023-03-15 13:04:59,805] [INFO] Total running time: 0h1m6s