[2023-03-16 06:03:26,035] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:03:26,035] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:03:26,035] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference
[2023-03-16 06:03:27,206] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:03:27,206] [INFO] Task started: Prodigal
[2023-03-16 06:03:27,206] [INFO] Running command: cat /var/lib/cwl/stgbe6cf045-9ee2-47e6-a47c-5562cf08de83/OceanDNA-b24784.fa | prodigal -d OceanDNA-b24784/cds.fna -a OceanDNA-b24784/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:03:57,222] [INFO] Task succeeded: Prodigal
[2023-03-16 06:03:57,222] [INFO] Task started: HMMsearch
[2023-03-16 06:03:57,223] [INFO] Running command: hmmsearch --tblout OceanDNA-b24784/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference/reference_markers.hmm OceanDNA-b24784/protein.faa > /dev/null
[2023-03-16 06:03:57,463] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:03:57,463] [INFO] Found 6/6 markers.
[2023-03-16 06:03:57,493] [INFO] Query marker FASTA was written to OceanDNA-b24784/markers.fasta
[2023-03-16 06:03:57,494] [INFO] Task started: Blastn
[2023-03-16 06:03:57,494] [INFO] Running command: blastn -query OceanDNA-b24784/markers.fasta -db /var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference/reference_markers.fasta -out OceanDNA-b24784/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:03:58,260] [INFO] Task succeeded: Blastn
[2023-03-16 06:03:58,262] [INFO] Selected 14 target genomes.
[2023-03-16 06:03:58,262] [INFO] Target genome list was writen to OceanDNA-b24784/target_genomes.txt
[2023-03-16 06:03:58,271] [INFO] Task started: fastANI
[2023-03-16 06:03:58,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6cf045-9ee2-47e6-a47c-5562cf08de83/OceanDNA-b24784.fa --refList OceanDNA-b24784/target_genomes.txt --output OceanDNA-b24784/fastani_result.tsv --threads 1
[2023-03-16 06:04:11,189] [INFO] Task succeeded: fastANI
[2023-03-16 06:04:11,190] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:04:11,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:04:11,198] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:04:11,198] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:04:11,198] [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
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	87.0352	1242	1606	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	86.9661	1237	1606	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	81.3667	1001	1606	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	81.2074	983	1606	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.3331	270	1606	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.2204	388	1606	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.3673	111	1606	95	below_threshold
Pedomonas mirosovicensis	strain=A1X5R2	GCA_022569295.1	2908641	2908641	type	True	76.3291	83	1606	95	below_threshold
Aestuariispira ectoiniformans	strain=SWCN16	GCA_025136295.1	2775080	2775080	type	True	76.2173	98	1606	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.1836	192	1606	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	76.0733	123	1606	95	below_threshold
Microvirga aerilata	strain=5420S-16	GCA_016743775.1	670292	670292	type	True	76.0101	111	1606	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.9902	92	1606	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.7445	111	1606	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:04:11,199] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24784/tc_result.tsv
[2023-03-16 06:04:11,199] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:04:11,199] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:04:11,199] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference/checkm_data
[2023-03-16 06:04:11,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:04:11,205] [INFO] Task started: CheckM
[2023-03-16 06:04:11,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24784/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24784/checkm_input OceanDNA-b24784/checkm_result
[2023-03-16 06:05:23,672] [INFO] Task succeeded: CheckM
[2023-03-16 06:05:23,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:05:23,704] [INFO] ===== Completeness check finished =====
[2023-03-16 06:05:23,704] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:05:23,704] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24784/markers.fasta)
[2023-03-16 06:05:23,705] [INFO] Task started: Blastn
[2023-03-16 06:05:23,705] [INFO] Running command: blastn -query OceanDNA-b24784/markers.fasta -db /var/lib/cwl/stgb3b81394-8527-4e2e-8d33-59bafd5c2fbd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24784/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:05:25,120] [INFO] Task succeeded: Blastn
[2023-03-16 06:05:25,121] [INFO] Selected 10 target genomes.
[2023-03-16 06:05:25,121] [INFO] Target genome list was writen to OceanDNA-b24784/target_genomes_gtdb.txt
[2023-03-16 06:05:25,131] [INFO] Task started: fastANI
[2023-03-16 06:05:25,132] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe6cf045-9ee2-47e6-a47c-5562cf08de83/OceanDNA-b24784.fa --refList OceanDNA-b24784/target_genomes_gtdb.txt --output OceanDNA-b24784/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:05:36,026] [INFO] Task succeeded: fastANI
[2023-03-16 06:05:36,032] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:05:36,033] [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_000426505.1	s__Nisaea denitrificans	87.0352	1242	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	86.9595	1238	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	81.4971	932	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	81.3425	1005	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	77.6897	426	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.2378	386	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	76.3673	111	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
GCF_016743775.1	s__Microvirga aerilata	76.0101	111	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003226555.1	s__Rhodopseudomonas palustris_I	75.9875	130	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195085.1	s__JACQAG01 sp016195085	75.9471	150	1606	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__JACQAG01	95.0	99.88	99.88	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:05:36,042] [INFO] GTDB search result was written to OceanDNA-b24784/result_gtdb.tsv
[2023-03-16 06:05:36,044] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:05:36,045] [INFO] DFAST_QC result json was written to OceanDNA-b24784/dqc_result.json
[2023-03-16 06:05:36,045] [INFO] DFAST_QC completed!
[2023-03-16 06:05:36,046] [INFO] Total running time: 0h2m10s