[2023-03-16 04:38:30,159] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,159] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,159] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference
[2023-03-16 04:38:31,250] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,250] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,250] [INFO] Running command: cat /var/lib/cwl/stg9edc2e85-11f7-4376-9fb4-1edaeb082cf1/OceanDNA-b20910.fa | prodigal -d OceanDNA-b20910/cds.fna -a OceanDNA-b20910/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:39:10,292] [INFO] Task succeeded: Prodigal
[2023-03-16 04:39:10,292] [INFO] Task started: HMMsearch
[2023-03-16 04:39:10,292] [INFO] Running command: hmmsearch --tblout OceanDNA-b20910/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference/reference_markers.hmm OceanDNA-b20910/protein.faa > /dev/null
[2023-03-16 04:39:10,600] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:39:10,600] [INFO] Found 6/6 markers.
[2023-03-16 04:39:10,655] [INFO] Query marker FASTA was written to OceanDNA-b20910/markers.fasta
[2023-03-16 04:39:10,656] [INFO] Task started: Blastn
[2023-03-16 04:39:10,656] [INFO] Running command: blastn -query OceanDNA-b20910/markers.fasta -db /var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference/reference_markers.fasta -out OceanDNA-b20910/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:39:11,266] [INFO] Task succeeded: Blastn
[2023-03-16 04:39:11,267] [INFO] Selected 27 target genomes.
[2023-03-16 04:39:11,267] [INFO] Target genome list was writen to OceanDNA-b20910/target_genomes.txt
[2023-03-16 04:39:11,304] [INFO] Task started: fastANI
[2023-03-16 04:39:11,304] [INFO] Running command: fastANI --query /var/lib/cwl/stg9edc2e85-11f7-4376-9fb4-1edaeb082cf1/OceanDNA-b20910.fa --refList OceanDNA-b20910/target_genomes.txt --output OceanDNA-b20910/fastani_result.tsv --threads 1
[2023-03-16 04:39:35,486] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:35,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:39:35,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:39:35,501] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:39:35,501] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:39:35,501] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.721	541	1985	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.7159	628	1985	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.6903	637	1985	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.0385	335	1985	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.8443	488	1985	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	74.7774	115	1985	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	74.7707	182	1985	95	below_threshold
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	74.7537	111	1985	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	74.7523	202	1985	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	74.7464	194	1985	95	below_threshold
Acidovorax valerianellae	strain=DSM 16619	GCA_900102625.1	187868	187868	type	True	74.7444	66	1985	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	74.7428	92	1985	95	below_threshold
Cellulomonas hominis	strain=DSM 9581	GCA_014201095.1	156981	156981	suspected-type	True	74.7142	203	1985	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	74.7139	123	1985	95	below_threshold
Cellulomonas hominis	strain=NBRC 16055	GCA_007989225.1	156981	156981	suspected-type	True	74.7075	200	1985	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	74.7043	202	1985	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	74.7008	205	1985	95	below_threshold
Microterricola viridarii	strain=DSM 21772	GCA_900104895.1	412690	412690	type	True	74.6918	138	1985	95	below_threshold
Ottowia beijingensis	strain=GCS-AN-3	GCA_013423955.1	1207057	1207057	type	True	74.6881	108	1985	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	74.6878	153	1985	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.6855	166	1985	95	below_threshold
Usitatibacter palustris	strain=Swamp67	GCA_013003985.1	2732487	2732487	type	True	74.67	92	1985	95	below_threshold
Methylobacterium tardum	strain=NBRC 103632	GCA_022179585.1	374432	374432	type	True	74.631	150	1985	95	below_threshold
Microbacterium radiodurans	strain=DSM 25564	GCA_008710705.1	661398	661398	type	True	74.63	148	1985	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	74.624	152	1985	95	below_threshold
Kineosporia rhizophila	strain=JCM 9960	GCA_021277265.1	84633	84633	type	True	74.6236	177	1985	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:39:35,501] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20910/tc_result.tsv
[2023-03-16 04:39:35,502] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:39:35,502] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:39:35,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference/checkm_data
[2023-03-16 04:39:35,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:39:35,513] [INFO] Task started: CheckM
[2023-03-16 04:39:35,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20910/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20910/checkm_input OceanDNA-b20910/checkm_result
[2023-03-16 04:41:07,868] [INFO] Task succeeded: CheckM
[2023-03-16 04:41:07,869] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.34%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:41:07,873] [INFO] ===== Completeness check finished =====
[2023-03-16 04:41:07,873] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:41:07,873] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20910/markers.fasta)
[2023-03-16 04:41:07,874] [INFO] Task started: Blastn
[2023-03-16 04:41:07,874] [INFO] Running command: blastn -query OceanDNA-b20910/markers.fasta -db /var/lib/cwl/stgd4a6ca0b-ab62-4ccc-a7f7-9d47cc5f5b8c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20910/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:41:08,882] [INFO] Task succeeded: Blastn
[2023-03-16 04:41:08,883] [INFO] Selected 18 target genomes.
[2023-03-16 04:41:08,883] [INFO] Target genome list was writen to OceanDNA-b20910/target_genomes_gtdb.txt
[2023-03-16 04:41:08,899] [INFO] Task started: fastANI
[2023-03-16 04:41:08,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg9edc2e85-11f7-4376-9fb4-1edaeb082cf1/OceanDNA-b20910.fa --refList OceanDNA-b20910/target_genomes_gtdb.txt --output OceanDNA-b20910/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:41:30,665] [INFO] Task succeeded: fastANI
[2023-03-16 04:41:30,674] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:41:30,674] [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_001464385.1	s__Ga0077550 sp001464385	76.4261	750	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	76.421	697	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCF_002994615.1	s__Enhygromyxa salina_A	75.784	517	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	75.6998	543	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	75.6947	348	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	75.6935	633	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000737335.2	s__Enhygromyxa salina_C	75.6215	416	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696955.1	s__J032 sp003696955	75.6056	189	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__J032	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	75.5016	502	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_016793465.1	s__Nannocystis sp016793465	75.4898	627	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826865.1	s__Ga0077550 sp902826865	75.439	289	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	75.1969	356	1985	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226565.1	s__PHBI01 sp006226565	74.8532	309	1985	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197205.1	s__JACPWG01 sp016197205	74.6332	162	1985	d__Bacteria;p__Planctomycetota;c__MHYJ01;o__WSZJ01;f__JACPWG01;g__JACPWG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140805.1	s__JABFRW01 sp013140805	74.5942	71	1985	d__Bacteria;p__Eisenbacteria;c__RBG-16-71-46;o__RBG-16-71-46;f__RBG-16-71-46;g__JABFRW01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:41:30,674] [INFO] GTDB search result was written to OceanDNA-b20910/result_gtdb.tsv
[2023-03-16 04:41:30,674] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:41:30,677] [INFO] DFAST_QC result json was written to OceanDNA-b20910/dqc_result.json
[2023-03-16 04:41:30,677] [INFO] DFAST_QC completed!
[2023-03-16 04:41:30,677] [INFO] Total running time: 0h3m1s