[2023-03-18 03:09:33,833] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:33,833] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:33,833] [INFO] DQC Reference Directory: /var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference
[2023-03-18 03:09:34,925] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:34,925] [INFO] Task started: Prodigal
[2023-03-18 03:09:34,925] [INFO] Running command: cat /var/lib/cwl/stg28cf9d94-512f-4387-bf85-2770fc2f90a2/OceanDNA-b30771.fa | prodigal -d OceanDNA-b30771/cds.fna -a OceanDNA-b30771/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:46,942] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:46,942] [INFO] Task started: HMMsearch
[2023-03-18 03:09:46,942] [INFO] Running command: hmmsearch --tblout OceanDNA-b30771/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference/reference_markers.hmm OceanDNA-b30771/protein.faa > /dev/null
[2023-03-18 03:09:47,125] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:47,126] [INFO] Found 6/6 markers.
[2023-03-18 03:09:47,144] [INFO] Query marker FASTA was written to OceanDNA-b30771/markers.fasta
[2023-03-18 03:09:47,144] [INFO] Task started: Blastn
[2023-03-18 03:09:47,144] [INFO] Running command: blastn -query OceanDNA-b30771/markers.fasta -db /var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference/reference_markers.fasta -out OceanDNA-b30771/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:47,858] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:47,859] [INFO] Selected 28 target genomes.
[2023-03-18 03:09:47,859] [INFO] Target genome list was writen to OceanDNA-b30771/target_genomes.txt
[2023-03-18 03:09:47,879] [INFO] Task started: fastANI
[2023-03-18 03:09:47,879] [INFO] Running command: fastANI --query /var/lib/cwl/stg28cf9d94-512f-4387-bf85-2770fc2f90a2/OceanDNA-b30771.fa --refList OceanDNA-b30771/target_genomes.txt --output OceanDNA-b30771/fastani_result.tsv --threads 1
[2023-03-18 03:10:09,777] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:09,777] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:10:09,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:10:09,792] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:10:09,792] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:10:09,792] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.8656	130	599	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.5693	87	599	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.5643	143	599	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.5375	146	599	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.4903	121	599	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.3881	132	599	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.3784	120	599	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2892	131	599	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.2834	103	599	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.2665	67	599	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.2386	98	599	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.2146	77	599	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.1255	74	599	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.9588	112	599	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.9495	73	599	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.9429	116	599	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.9067	119	599	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.8996	70	599	95	below_threshold
Roseospira marina	strain=DSM 15113	GCA_014203135.1	140057	140057	type	True	75.8871	61	599	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	75.8709	101	599	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8014	139	599	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.725	96	599	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.7188	79	599	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.6138	113	599	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	75.5869	66	599	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	75.5271	89	599	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.526	70	599	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:10:09,792] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30771/tc_result.tsv
[2023-03-18 03:10:09,792] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:10:09,792] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:10:09,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference/checkm_data
[2023-03-18 03:10:09,793] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:10:09,797] [INFO] Task started: CheckM
[2023-03-18 03:10:09,797] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30771/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30771/checkm_input OceanDNA-b30771/checkm_result
[2023-03-18 03:10:42,750] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:42,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.96%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:42,753] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:42,753] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:42,753] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30771/markers.fasta)
[2023-03-18 03:10:42,753] [INFO] Task started: Blastn
[2023-03-18 03:10:42,753] [INFO] Running command: blastn -query OceanDNA-b30771/markers.fasta -db /var/lib/cwl/stge0874f6d-1f8a-449a-aa3d-e96ee516bb26/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30771/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:44,126] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:44,127] [INFO] Selected 29 target genomes.
[2023-03-18 03:10:44,127] [INFO] Target genome list was writen to OceanDNA-b30771/target_genomes_gtdb.txt
[2023-03-18 03:10:44,231] [INFO] Task started: fastANI
[2023-03-18 03:10:44,232] [INFO] Running command: fastANI --query /var/lib/cwl/stg28cf9d94-512f-4387-bf85-2770fc2f90a2/OceanDNA-b30771.fa --refList OceanDNA-b30771/target_genomes_gtdb.txt --output OceanDNA-b30771/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:11:06,091] [INFO] Task succeeded: fastANI
[2023-03-18 03:11:06,106] [INFO] Found 29 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:11:06,106] [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_002690215.1	s__GCA-2690215 sp002690215	78.4744	89	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187325.1	s__JACPJY01 sp016187325	77.1342	129	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__JACPJY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	77.1063	83	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.0886	123	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.9523	137	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	76.8233	115	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.7153	131	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	76.5718	88	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.534	145	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000009985.1	s__Phaeospirillum magneticum	76.5052	101	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001830425.1	s__2-02-FULL-58-16 sp001830425	76.4182	75	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-02-FULL-58-16;g__2-02-FULL-58-16	95.0	99.96	99.96	0.97	0.97	2	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.4093	142	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.4034	131	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941105.1	s__CAJANL01 sp903941105	76.2689	114	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAJANL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016583645.1	s__Rhodovibrio sodomensis	76.2588	75	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Rhodovibrionaceae;g__Rhodovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016212565.1	s__JACRFY01 sp016212565	76.2567	101	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JACRFY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018432935.1	s__JAHDSF01 sp018432935	76.2148	122	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JAHDSF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694025.1	s__SHVZ01 sp009694025	76.1256	71	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829825.1	s__Phaeospirillum magnetotacticum	76.1255	74	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869285.1	s__SHVZ01 sp016869285	76.1183	81	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	76.0722	106	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869415.1	s__VGEI01 sp016869415	76.0147	79	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.0072	106	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016806835.1	s__Skermanella rosea	75.9987	109	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	75.9495	73	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_016869375.1	s__SHVZ01 sp016869375	75.7683	85	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	75.7283	95	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712595.1	s__SSA4 sp016712595	75.7184	60	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.6738	108	599	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:11:06,107] [INFO] GTDB search result was written to OceanDNA-b30771/result_gtdb.tsv
[2023-03-18 03:11:06,107] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:11:06,109] [INFO] DFAST_QC result json was written to OceanDNA-b30771/dqc_result.json
[2023-03-18 03:11:06,110] [INFO] DFAST_QC completed!
[2023-03-18 03:11:06,110] [INFO] Total running time: 0h1m32s