[2023-06-19 06:45:37,133] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:45:37,136] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:45:37,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference
[2023-06-19 06:45:38,386] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:45:38,387] [INFO] Task started: Prodigal
[2023-06-19 06:45:38,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg4266b3ca-1f84-4a7f-b6f2-8fe6bb882022/GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:45:51,611] [INFO] Task succeeded: Prodigal
[2023-06-19 06:45:51,611] [INFO] Task started: HMMsearch
[2023-06-19 06:45:51,611] [INFO] Running command: hmmsearch --tblout GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference/reference_markers.hmm GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:45:51,861] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:45:51,862] [INFO] Found 6/6 markers.
[2023-06-19 06:45:51,912] [INFO] Query marker FASTA was written to GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 06:45:51,912] [INFO] Task started: Blastn
[2023-06-19 06:45:51,912] [INFO] Running command: blastn -query GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference/reference_markers.fasta -out GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:45:52,669] [INFO] Task succeeded: Blastn
[2023-06-19 06:45:52,672] [INFO] Selected 33 target genomes.
[2023-06-19 06:45:52,673] [INFO] Target genome list was writen to GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 06:45:52,676] [INFO] Task started: fastANI
[2023-06-19 06:45:52,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg4266b3ca-1f84-4a7f-b6f2-8fe6bb882022/GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:46:20,403] [INFO] Task succeeded: fastANI
[2023-06-19 06:46:20,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:46:20,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:46:20,423] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:46:20,423] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 06:46:20,423] [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
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	75.3777	58	1644	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	75.2718	94	1644	95	below_threshold
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.2491	100	1644	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.247	104	1644	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.2432	103	1644	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	75.1951	94	1644	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	75.1734	96	1644	95	below_threshold
Zavarzinia aquatilis	strain=HR-AS	GCA_003173035.1	2211142	2211142	type	True	75.1233	83	1644	95	below_threshold
Thiohalospira halophila	strain=HL 3	GCA_900112605.1	381300	381300	type	True	75.0649	66	1644	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	75.0645	61	1644	95	below_threshold
Amaricoccus macauensis	strain=DSM 101730	GCA_014201905.1	57001	57001	type	True	75.0561	79	1644	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	75.0207	183	1644	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	74.9432	62	1644	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_003387095.1	48	48	type	True	74.9245	195	1644	95	below_threshold
Archangium gephyra	strain=DSM 2261	GCA_001027285.1	48	48	type	True	74.9149	200	1644	95	below_threshold
Peterkaempfera bronchialis	strain=DSM 106435	GCA_003258605.2	2126346	2126346	type	True	74.9135	137	1644	95	below_threshold
Streptomyces morookaense	strain=DSM 40503	GCA_013030945.1	1970	1970	type	True	74.8926	129	1644	95	below_threshold
Novosphingobium rosa	strain=NBRC 15208	GCA_001598555.1	76978	76978	type	True	74.8868	60	1644	95	below_threshold
Streptomyces morookaense	strain=JCM 4793	GCA_014656115.1	1970	1970	type	True	74.8809	133	1644	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	74.8685	153	1644	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	74.827	133	1644	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	74.8121	150	1644	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	74.809	125	1644	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	74.7627	174	1644	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	74.7623	174	1644	95	below_threshold
Saccharopolyspora gloriosae	strain=DSM 45582	GCA_014203325.1	455344	455344	type	True	74.6598	128	1644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 06:46:20,425] [INFO] DFAST Taxonomy check result was written to GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 06:46:20,425] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:46:20,425] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:46:20,426] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference/checkm_data
[2023-06-19 06:46:20,427] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:46:20,476] [INFO] Task started: CheckM
[2023-06-19 06:46:20,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 06:47:00,140] [INFO] Task succeeded: CheckM
[2023-06-19 06:47:00,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 11.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:47:00,160] [INFO] ===== Completeness check finished =====
[2023-06-19 06:47:00,161] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:47:00,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 06:47:00,161] [INFO] Task started: Blastn
[2023-06-19 06:47:00,161] [INFO] Running command: blastn -query GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6aaac23f-55b1-436f-8d9c-54f1ee27cbda/dqc_reference/reference_markers_gtdb.fasta -out GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:47:01,526] [INFO] Task succeeded: Blastn
[2023-06-19 06:47:01,529] [INFO] Selected 25 target genomes.
[2023-06-19 06:47:01,530] [INFO] Target genome list was writen to GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:47:01,538] [INFO] Task started: fastANI
[2023-06-19 06:47:01,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg4266b3ca-1f84-4a7f-b6f2-8fe6bb882022/GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:47:16,478] [INFO] Task succeeded: fastANI
[2023-06-19 06:47:16,493] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 06:47:16,493] [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_002420005.1	s__UBA5704 sp002420005	76.7204	375	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699405.1	s__JAAYLR01 sp016699405	76.6698	285	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525905.1	s__JACTMI01 sp011525905	76.5604	268	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012521815.1	s__JAAYLR01 sp012521815	76.5255	206	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01	95.0	99.12	98.38	0.89	0.78	5	-
GCA_017860005.1	s__JACTMI01 sp017860005	76.4814	246	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697015.1	s__J023 sp003697015	76.4386	356	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014584695.1	s__JACTMI01 sp014584695	76.4294	272	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018057705.1	s__JAGPDF01 sp018057705	76.3875	235	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01	95.0	99.73	99.73	0.94	0.94	2	-
GCA_905479655.1	s__CAJQNK01 sp905479655	76.1153	207	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__CAJQNK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003388555.1	s__QQVD01 sp003388555	76.1107	256	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_011525365.1	s__WTGL01 sp011525365	76.11	130	1644	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	75.2723	94	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	75.2706	89	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_014193375.1	s__Halomonas campaniensis	75.1535	117	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173035.1	s__Zavarzinia aquatilis	75.1307	82	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Zavarziniales;f__Zavarziniaceae;g__Zavarzinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	75.1199	58	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004001245.1	s__Sulfurivermis fontis	75.0533	53	1644	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalomonadales;f__Thiohalomonadaceae;g__Sulfurivermis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598555.1	s__Novosphingobium rosa	74.8957	59	1644	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:47:16,495] [INFO] GTDB search result was written to GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 06:47:16,496] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:47:16,500] [INFO] DFAST_QC result json was written to GCA_937867335.1_SRR1772176_bin.111_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 06:47:16,500] [INFO] DFAST_QC completed!
[2023-06-19 06:47:16,501] [INFO] Total running time: 0h1m39s