[2023-03-15 18:12:37,904] [INFO] DFAST_QC pipeline started.
[2023-03-15 18:12:37,905] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 18:12:37,905] [INFO] DQC Reference Directory: /var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference
[2023-03-15 18:12:39,779] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 18:12:39,779] [INFO] Task started: Prodigal
[2023-03-15 18:12:39,780] [INFO] Running command: cat /var/lib/cwl/stgcc7df231-5c38-4a2c-a6a5-06e73ba86678/OceanDNA-b32720.fa | prodigal -d OceanDNA-b32720/cds.fna -a OceanDNA-b32720/protein.faa -g 11 -q > /dev/null
[2023-03-15 18:13:00,118] [INFO] Task succeeded: Prodigal
[2023-03-15 18:13:00,119] [INFO] Task started: HMMsearch
[2023-03-15 18:13:00,119] [INFO] Running command: hmmsearch --tblout OceanDNA-b32720/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference/reference_markers.hmm OceanDNA-b32720/protein.faa > /dev/null
[2023-03-15 18:13:00,301] [INFO] Task succeeded: HMMsearch
[2023-03-15 18:13:00,301] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcc7df231-5c38-4a2c-a6a5-06e73ba86678/OceanDNA-b32720.fa]
[2023-03-15 18:13:00,327] [INFO] Query marker FASTA was written to OceanDNA-b32720/markers.fasta
[2023-03-15 18:13:00,331] [INFO] Task started: Blastn
[2023-03-15 18:13:00,331] [INFO] Running command: blastn -query OceanDNA-b32720/markers.fasta -db /var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference/reference_markers.fasta -out OceanDNA-b32720/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:13:00,848] [INFO] Task succeeded: Blastn
[2023-03-15 18:13:00,848] [INFO] Selected 20 target genomes.
[2023-03-15 18:13:00,849] [INFO] Target genome list was writen to OceanDNA-b32720/target_genomes.txt
[2023-03-15 18:13:00,963] [INFO] Task started: fastANI
[2023-03-15 18:13:00,964] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7df231-5c38-4a2c-a6a5-06e73ba86678/OceanDNA-b32720.fa --refList OceanDNA-b32720/target_genomes.txt --output OceanDNA-b32720/fastani_result.tsv --threads 1
[2023-03-15 18:13:17,982] [INFO] Task succeeded: fastANI
[2023-03-15 18:13:17,983] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 18:13:17,983] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 18:13:17,995] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 18:13:17,995] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 18:13:17,995] [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 acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3128	139	1104	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.2434	241	1104	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.2344	208	1104	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.1874	215	1104	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.9792	103	1104	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.9328	180	1104	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	75.9266	193	1104	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.9054	102	1104	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.8346	187	1104	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	75.8173	160	1104	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.6706	195	1104	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	75.6351	122	1104	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	75.5798	217	1104	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	75.5494	124	1104	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.5373	107	1104	95	below_threshold
Sphingomonas sabuli	strain=sand1-3	GCA_014352855.1	2764186	2764186	type	True	75.4043	70	1104	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.1495	107	1104	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	75.1325	59	1104	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	75.116	89	1104	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	75.1135	89	1104	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 18:13:17,995] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32720/tc_result.tsv
[2023-03-15 18:13:17,995] [INFO] ===== Taxonomy check completed =====
[2023-03-15 18:13:17,995] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 18:13:17,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference/checkm_data
[2023-03-15 18:13:17,996] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 18:13:18,001] [INFO] Task started: CheckM
[2023-03-15 18:13:18,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32720/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32720/checkm_input OceanDNA-b32720/checkm_result
[2023-03-15 18:14:08,156] [INFO] Task succeeded: CheckM
[2023-03-15 18:14:08,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.59%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 18:14:08,159] [INFO] ===== Completeness check finished =====
[2023-03-15 18:14:08,159] [INFO] ===== Start GTDB Search =====
[2023-03-15 18:14:08,159] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32720/markers.fasta)
[2023-03-15 18:14:08,161] [INFO] Task started: Blastn
[2023-03-15 18:14:08,161] [INFO] Running command: blastn -query OceanDNA-b32720/markers.fasta -db /var/lib/cwl/stgeb6ef457-d3fc-478b-b29c-31e7bfbd0aa1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32720/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 18:14:08,795] [INFO] Task succeeded: Blastn
[2023-03-15 18:14:08,796] [INFO] Selected 17 target genomes.
[2023-03-15 18:14:08,796] [INFO] Target genome list was writen to OceanDNA-b32720/target_genomes_gtdb.txt
[2023-03-15 18:14:08,904] [INFO] Task started: fastANI
[2023-03-15 18:14:08,904] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc7df231-5c38-4a2c-a6a5-06e73ba86678/OceanDNA-b32720.fa --refList OceanDNA-b32720/target_genomes_gtdb.txt --output OceanDNA-b32720/fastani_result_gtdb.tsv --threads 1
[2023-03-15 18:14:21,324] [INFO] Task succeeded: fastANI
[2023-03-15 18:14:21,333] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 18:14:21,334] [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
GCA_018702955.1	s__UBA8079 sp018702955	77.1236	227	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_011087645.1	s__JABDJY01 sp011087645	77.0974	252	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	99.97	99.97	0.97	0.97	2	-
GCA_018667335.1	s__UBA8079 sp018667335	77.0811	241	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_013003285.1	s__JABDJY01 sp013003285	77.0402	223	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABDJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727315.1	s__UBA8079 sp002727315	76.9605	177	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.4254	178	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.0721	156	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903853455.1	s__Phaeospirillum sp903853455	76.0151	144	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	99.97	99.97	0.98	0.98	2	-
GCA_001657395.1	s__Pelagibius sp001657395	75.9893	143	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__Pelagibius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011022235.1	s__Magnetospirillum aberrantis	75.9054	102	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729425.1	s__Phaeospirillum sp902729425	75.8839	152	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903860935.1	s__CAIOSQ01 sp903860935	75.832	161	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	75.8078	163	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971625.1	s__Bradyrhizobium sp018971625	75.7553	68	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Bradyrhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899065.1	s__Devosia_A sp001899065	75.5982	106	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.96	98.00	0.93	0.88	3	-
--------------------------------------------------------------------------------
[2023-03-15 18:14:21,334] [INFO] GTDB search result was written to OceanDNA-b32720/result_gtdb.tsv
[2023-03-15 18:14:21,334] [INFO] ===== GTDB Search completed =====
[2023-03-15 18:14:21,336] [INFO] DFAST_QC result json was written to OceanDNA-b32720/dqc_result.json
[2023-03-15 18:14:21,336] [INFO] DFAST_QC completed!
[2023-03-15 18:14:21,336] [INFO] Total running time: 0h1m43s