[2023-03-15 21:01:44,345] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,345] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,701] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,702] [INFO] Running command: cat /var/lib/cwl/stg231c17ba-1fe1-4e55-9a11-ec304a5127e2/OceanDNA-b503.fa | prodigal -d OceanDNA-b503/cds.fna -a OceanDNA-b503/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:01:58,647] [INFO] Task succeeded: Prodigal
[2023-03-15 21:01:58,648] [INFO] Task started: HMMsearch
[2023-03-15 21:01:58,648] [INFO] Running command: hmmsearch --tblout OceanDNA-b503/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference/reference_markers.hmm OceanDNA-b503/protein.faa > /dev/null
[2023-03-15 21:01:58,811] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:01:58,811] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg231c17ba-1fe1-4e55-9a11-ec304a5127e2/OceanDNA-b503.fa]
[2023-03-15 21:01:58,831] [INFO] Query marker FASTA was written to OceanDNA-b503/markers.fasta
[2023-03-15 21:01:58,831] [INFO] Task started: Blastn
[2023-03-15 21:01:58,831] [INFO] Running command: blastn -query OceanDNA-b503/markers.fasta -db /var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference/reference_markers.fasta -out OceanDNA-b503/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:01:59,300] [INFO] Task succeeded: Blastn
[2023-03-15 21:01:59,301] [INFO] Selected 13 target genomes.
[2023-03-15 21:01:59,301] [INFO] Target genome list was writen to OceanDNA-b503/target_genomes.txt
[2023-03-15 21:01:59,309] [INFO] Task started: fastANI
[2023-03-15 21:01:59,309] [INFO] Running command: fastANI --query /var/lib/cwl/stg231c17ba-1fe1-4e55-9a11-ec304a5127e2/OceanDNA-b503.fa --refList OceanDNA-b503/target_genomes.txt --output OceanDNA-b503/fastani_result.tsv --threads 1
[2023-03-15 21:02:10,636] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:10,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:10,636] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:10,644] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:10,644] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:10,644] [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
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	78.9051	341	655	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	78.1842	257	655	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.9611	239	655	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.9688	202	655	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.3138	129	655	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.1465	113	655	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	75.117	53	655	95	below_threshold
Klenkia marina	strain=DSM 45722	GCA_900101025.1	1960309	1960309	type	True	75.0901	76	655	95	below_threshold
Streptomyces roseolus	strain=JCM 4411	GCA_014649855.1	67358	67358	type	True	75.0548	84	655	95	below_threshold
Streptomyces himalayensis subsp. aureolus	strain=PSKA54	GCA_013912435.1	2758039	2820085	type	True	75.0129	66	655	95	below_threshold
Streptomyces omiyaensis	strain=JCM 4806	GCA_014650895.1	68247	68247	type	True	75.0071	103	655	95	below_threshold
Streptomyces himalayensis subsp. himalayensis	strain=PSKA28	GCA_013778455.1	2756131	2820085	type	True	74.9065	71	655	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:10,644] [INFO] DFAST Taxonomy check result was written to OceanDNA-b503/tc_result.tsv
[2023-03-15 21:02:10,644] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:10,644] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:10,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference/checkm_data
[2023-03-15 21:02:10,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:10,650] [INFO] Task started: CheckM
[2023-03-15 21:02:10,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b503/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b503/checkm_input OceanDNA-b503/checkm_result
[2023-03-15 21:02:46,022] [INFO] Task succeeded: CheckM
[2023-03-15 21:02:46,022] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.03%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:02:46,024] [INFO] ===== Completeness check finished =====
[2023-03-15 21:02:46,024] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:02:46,025] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b503/markers.fasta)
[2023-03-15 21:02:46,025] [INFO] Task started: Blastn
[2023-03-15 21:02:46,025] [INFO] Running command: blastn -query OceanDNA-b503/markers.fasta -db /var/lib/cwl/stgfca17fff-e686-4275-b094-1506d5b07f12/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b503/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:46,517] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:46,518] [INFO] Selected 14 target genomes.
[2023-03-15 21:02:46,518] [INFO] Target genome list was writen to OceanDNA-b503/target_genomes_gtdb.txt
[2023-03-15 21:02:46,869] [INFO] Task started: fastANI
[2023-03-15 21:02:46,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg231c17ba-1fe1-4e55-9a11-ec304a5127e2/OceanDNA-b503.fa --refList OceanDNA-b503/target_genomes_gtdb.txt --output OceanDNA-b503/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:02:56,393] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:56,403] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:02:56,403] [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_000348785.1	s__Ilumatobacter_A coccineus	78.931	339	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	78.1929	257	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	78.0416	220	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.9772	238	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	77.4119	176	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	77.4116	193	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	77.3009	166	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCF_003426815.1	s__Desertimonas flava	76.9944	200	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_015767405.1	s__Sva-07 sp015767405	76.8211	98	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010024485.1	s__Casp-actino5 sp010024485	76.5175	69	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_019090765.1	s__Sva-07 sp019090765	76.1637	52	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185275.1	s__JACPNX01 sp016185275	76.0207	93	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JACPNX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794585.1	s__JAEUJM01 sp016794585	75.8865	121	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAEUJM01;g__JAEUJM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005888395.1	s__AC-25 sp005888395	75.806	61	655	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-25;g__AC-25	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:02:56,403] [INFO] GTDB search result was written to OceanDNA-b503/result_gtdb.tsv
[2023-03-15 21:02:56,403] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:02:56,405] [INFO] DFAST_QC result json was written to OceanDNA-b503/dqc_result.json
[2023-03-15 21:02:56,405] [INFO] DFAST_QC completed!
[2023-03-15 21:02:56,405] [INFO] Total running time: 0h1m12s