[2023-06-08 09:05:12,721] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:05:12,724] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:05:12,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference
[2023-06-08 09:05:14,669] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:05:14,670] [INFO] Task started: Prodigal
[2023-06-08 09:05:14,670] [INFO] Running command: gunzip -c /var/lib/cwl/stg888c404b-ff77-42c0-9907-31e81632dd11/GCA_945903685.1_TH-11nov19-65_genomic.fna.gz | prodigal -d GCA_945903685.1_TH-11nov19-65_genomic.fna/cds.fna -a GCA_945903685.1_TH-11nov19-65_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:05:20,343] [INFO] Task succeeded: Prodigal
[2023-06-08 09:05:20,344] [INFO] Task started: HMMsearch
[2023-06-08 09:05:20,344] [INFO] Running command: hmmsearch --tblout GCA_945903685.1_TH-11nov19-65_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference/reference_markers.hmm GCA_945903685.1_TH-11nov19-65_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:05:20,572] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:05:20,573] [INFO] Found 6/6 markers.
[2023-06-08 09:05:20,601] [INFO] Query marker FASTA was written to GCA_945903685.1_TH-11nov19-65_genomic.fna/markers.fasta
[2023-06-08 09:05:20,601] [INFO] Task started: Blastn
[2023-06-08 09:05:20,601] [INFO] Running command: blastn -query GCA_945903685.1_TH-11nov19-65_genomic.fna/markers.fasta -db /var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference/reference_markers.fasta -out GCA_945903685.1_TH-11nov19-65_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:05:21,440] [INFO] Task succeeded: Blastn
[2023-06-08 09:05:21,445] [INFO] Selected 34 target genomes.
[2023-06-08 09:05:21,446] [INFO] Target genome list was writen to GCA_945903685.1_TH-11nov19-65_genomic.fna/target_genomes.txt
[2023-06-08 09:05:21,456] [INFO] Task started: fastANI
[2023-06-08 09:05:21,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg888c404b-ff77-42c0-9907-31e81632dd11/GCA_945903685.1_TH-11nov19-65_genomic.fna.gz --refList GCA_945903685.1_TH-11nov19-65_genomic.fna/target_genomes.txt --output GCA_945903685.1_TH-11nov19-65_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:05:47,266] [INFO] Task succeeded: fastANI
[2023-06-08 09:05:47,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:05:47,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:05:47,289] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:05:47,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 09:05:47,290] [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
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	76.4488	121	689	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.4011	152	689	95	below_threshold
Hypericibacter terrae	strain=R5913	GCA_008728855.1	2602015	2602015	type	True	76.3325	134	689	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.3293	160	689	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.3205	159	689	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	76.177	145	689	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	76.1758	69	689	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.1586	125	689	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.1449	126	689	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1394	162	689	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	76.0981	116	689	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.0734	134	689	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	76.0278	131	689	95	below_threshold
Bradyrhizobium japonicum	strain=NBRC 14783	GCA_006539645.1	375	375	type	True	75.9813	115	689	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.9753	139	689	95	below_threshold
Bradyrhizobium japonicum	strain=USDA 6	GCA_000472985.1	375	375	type	True	75.9713	116	689	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	75.9318	57	689	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	75.8631	133	689	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	75.8277	122	689	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.8253	164	689	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	75.7052	69	689	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	75.7003	57	689	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	75.6947	93	689	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	75.6496	60	689	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	75.609	118	689	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	75.5567	99	689	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	75.4545	84	689	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	75.4274	52	689	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	75.1933	78	689	95	below_threshold
Agrococcus pavilionensis	strain=RW1	GCA_000400485.1	1346502	1346502	type	True	74.763	50	689	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 09:05:47,292] [INFO] DFAST Taxonomy check result was written to GCA_945903685.1_TH-11nov19-65_genomic.fna/tc_result.tsv
[2023-06-08 09:05:47,293] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:05:47,293] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:05:47,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference/checkm_data
[2023-06-08 09:05:47,295] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:05:47,328] [INFO] Task started: CheckM
[2023-06-08 09:05:47,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945903685.1_TH-11nov19-65_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945903685.1_TH-11nov19-65_genomic.fna/checkm_input GCA_945903685.1_TH-11nov19-65_genomic.fna/checkm_result
[2023-06-08 09:06:09,906] [INFO] Task succeeded: CheckM
[2023-06-08 09:06:09,908] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:06:09,927] [INFO] ===== Completeness check finished =====
[2023-06-08 09:06:09,927] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:06:09,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945903685.1_TH-11nov19-65_genomic.fna/markers.fasta)
[2023-06-08 09:06:09,928] [INFO] Task started: Blastn
[2023-06-08 09:06:09,928] [INFO] Running command: blastn -query GCA_945903685.1_TH-11nov19-65_genomic.fna/markers.fasta -db /var/lib/cwl/stg4862f2f5-98a7-4ca7-85d6-5f9f1dc003b1/dqc_reference/reference_markers_gtdb.fasta -out GCA_945903685.1_TH-11nov19-65_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:06:11,333] [INFO] Task succeeded: Blastn
[2023-06-08 09:06:11,339] [INFO] Selected 28 target genomes.
[2023-06-08 09:06:11,339] [INFO] Target genome list was writen to GCA_945903685.1_TH-11nov19-65_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:06:11,416] [INFO] Task started: fastANI
[2023-06-08 09:06:11,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg888c404b-ff77-42c0-9907-31e81632dd11/GCA_945903685.1_TH-11nov19-65_genomic.fna.gz --refList GCA_945903685.1_TH-11nov19-65_genomic.fna/target_genomes_gtdb.txt --output GCA_945903685.1_TH-11nov19-65_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:06:30,126] [INFO] Task succeeded: fastANI
[2023-06-08 09:06:30,155] [INFO] Found 28 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 09:06:30,156] [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_016869275.1	s__SHVV01 sp016869275	90.3561	575	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVV01;f__SHVV01;g__SHVV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694095.1	s__SHVV01 sp009694095	77.8514	154	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVV01;f__SHVV01;g__SHVV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869765.1	s__SHVP01 sp016869765	77.0702	93	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVP01;f__SHVP01;g__SHVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.6989	108	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	76.6903	198	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694165.1	s__SHVP01 sp009694165	76.6426	55	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVP01;f__SHVP01;g__SHVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.5531	158	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	76.4541	108	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826565.1	s__CADEFF01 sp902826565	76.3807	125	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__CADEFF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869195.1	s__SHWC01 sp016869195	76.3485	92	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__SHWC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694025.1	s__SHVZ01 sp009694025	76.3477	97	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305635.1	s__Bauldia sp017305635	76.3433	105	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.3237	162	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.3187	161	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	76.3108	134	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.2474	89	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177515.1	s__Azospirillum oryzae_A	76.2397	134	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	76.1576	125	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011523425.1	s__WTGU01 sp011523425	76.1497	111	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA828;f__UBA828;g__WTGU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307275.1	s__Reyranella sp017307275	76.0982	101	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690215.1	s__GCA-2690215 sp002690215	76.0858	85	689	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_903907895.1	s__CAIVPW01 sp903907895	76.0664	64	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CAIVPW01;f__CAIVPW01;g__CAIVPW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694045.1	s__SHVY01 sp009694045	76.0661	94	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SP197;f__SP197;g__SHVY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	75.9285	86	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	75.8255	164	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	75.817	65	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013359755.1	s__Tardiphaga robiniae	75.8101	73	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Tardiphaga	95.0	96.54	96.42	0.88	0.87	5	-
GCA_017983635.1	s__SZUA-430 sp017983635	75.8088	61	689	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__SZUA-430	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:06:30,166] [INFO] GTDB search result was written to GCA_945903685.1_TH-11nov19-65_genomic.fna/result_gtdb.tsv
[2023-06-08 09:06:30,167] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:06:30,173] [INFO] DFAST_QC result json was written to GCA_945903685.1_TH-11nov19-65_genomic.fna/dqc_result.json
[2023-06-08 09:06:30,173] [INFO] DFAST_QC completed!
[2023-06-08 09:06:30,174] [INFO] Total running time: 0h1m17s