[2023-03-16 23:05:03,858] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:05:03,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:05:03,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference
[2023-03-16 23:05:05,095] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:05:05,096] [INFO] Task started: Prodigal
[2023-03-16 23:05:05,096] [INFO] Running command: cat /var/lib/cwl/stg176149fe-3089-4afd-9b8b-81003889e75c/OceanDNA-b31005.fa | prodigal -d OceanDNA-b31005/cds.fna -a OceanDNA-b31005/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:05:31,679] [INFO] Task succeeded: Prodigal
[2023-03-16 23:05:31,679] [INFO] Task started: HMMsearch
[2023-03-16 23:05:31,679] [INFO] Running command: hmmsearch --tblout OceanDNA-b31005/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference/reference_markers.hmm OceanDNA-b31005/protein.faa > /dev/null
[2023-03-16 23:05:31,928] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:05:31,928] [INFO] Found 6/6 markers.
[2023-03-16 23:05:31,953] [INFO] Query marker FASTA was written to OceanDNA-b31005/markers.fasta
[2023-03-16 23:05:31,953] [INFO] Task started: Blastn
[2023-03-16 23:05:31,954] [INFO] Running command: blastn -query OceanDNA-b31005/markers.fasta -db /var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference/reference_markers.fasta -out OceanDNA-b31005/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:05:32,840] [INFO] Task succeeded: Blastn
[2023-03-16 23:05:32,841] [INFO] Selected 28 target genomes.
[2023-03-16 23:05:32,842] [INFO] Target genome list was writen to OceanDNA-b31005/target_genomes.txt
[2023-03-16 23:05:32,859] [INFO] Task started: fastANI
[2023-03-16 23:05:32,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg176149fe-3089-4afd-9b8b-81003889e75c/OceanDNA-b31005.fa --refList OceanDNA-b31005/target_genomes.txt --output OceanDNA-b31005/fastani_result.tsv --threads 1
[2023-03-16 23:05:54,561] [INFO] Task succeeded: fastANI
[2023-03-16 23:05:54,562] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:05:54,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:05:54,577] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:05:54,577] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:05:54,577] [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
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.8513	198	1275	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.8423	176	1275	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.822	192	1275	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.7439	192	1275	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.732	228	1275	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.6846	208	1275	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.5811	182	1275	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.5488	98	1275	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.5448	199	1275	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	76.5336	224	1275	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.521	176	1275	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.4898	259	1275	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.4422	214	1275	95	below_threshold
Dongia mobilis	strain=CGMCC 1.7660	GCA_004363235.1	578943	578943	type	True	76.3974	137	1275	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	76.3583	134	1275	95	below_threshold
Zavarzinia compransoris	strain=DSM 1231	GCA_003173055.1	1264899	1264899	type	True	76.3296	215	1275	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2899	240	1275	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.2293	206	1275	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.2145	248	1275	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.2141	212	1275	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.1506	188	1275	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	76.1498	72	1275	95	below_threshold
Magnetospirillum molischianum	strain=DSM 120	GCA_000294655.1	1083	1083	type	True	75.9294	94	1275	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	75.8673	111	1275	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	75.841	124	1275	95	below_threshold
Methylorubrum podarium	strain=DSM 15083	GCA_022179745.1	200476	200476	type	True	75.7809	101	1275	95	below_threshold
Roseomonas oryzae	strain=KCTC 42542	GCA_008386565.1	1608942	1608942	type	True	75.7333	142	1275	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	75.4693	91	1275	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:05:54,578] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31005/tc_result.tsv
[2023-03-16 23:05:54,578] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:05:54,579] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:05:54,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference/checkm_data
[2023-03-16 23:05:54,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:05:54,594] [INFO] Task started: CheckM
[2023-03-16 23:05:54,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31005/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31005/checkm_input OceanDNA-b31005/checkm_result
[2023-03-16 23:06:57,725] [INFO] Task succeeded: CheckM
[2023-03-16 23:06:57,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:06:57,728] [INFO] ===== Completeness check finished =====
[2023-03-16 23:06:57,728] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:06:57,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31005/markers.fasta)
[2023-03-16 23:06:57,729] [INFO] Task started: Blastn
[2023-03-16 23:06:57,729] [INFO] Running command: blastn -query OceanDNA-b31005/markers.fasta -db /var/lib/cwl/stg490a0611-64ec-42e1-a797-3401098f593b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31005/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:06:59,444] [INFO] Task succeeded: Blastn
[2023-03-16 23:06:59,445] [INFO] Selected 11 target genomes.
[2023-03-16 23:06:59,445] [INFO] Target genome list was writen to OceanDNA-b31005/target_genomes_gtdb.txt
[2023-03-16 23:06:59,914] [INFO] Task started: fastANI
[2023-03-16 23:06:59,914] [INFO] Running command: fastANI --query /var/lib/cwl/stg176149fe-3089-4afd-9b8b-81003889e75c/OceanDNA-b31005.fa --refList OceanDNA-b31005/target_genomes_gtdb.txt --output OceanDNA-b31005/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:07:08,346] [INFO] Task succeeded: fastANI
[2023-03-16 23:07:08,353] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 23:07:08,354] [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_002706405.1	s__UBA1479 sp002706405	99.8713	1118	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	conclusive
GCA_002325375.1	s__UBA1479 sp002325375	89.4459	1112	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002781745.1	s__UBA1479 sp002781745	83.999	844	1275	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_002696205.1	s__UBA1479 sp002696205	82.7458	795	1275	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_002433335.1	s__UBA1479 sp002433335	81.3155	746	1275	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_002686255.1	s__Casp-alpha2 sp002686255	77.4352	237	1275	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_017640505.1	s__UBA4479 sp017640505	77.3485	232	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017644185.1	s__UBA4479 sp017644185	76.8651	219	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650715.1	s__Phaeospirillum marisnigri	76.8027	179	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009985.1	s__Phaeospirillum magneticum	76.7609	195	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513295.1	s__Magnetospirillum gryphiswaldense	76.7318	193	1275	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	97.87	97.87	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2023-03-16 23:07:08,354] [INFO] GTDB search result was written to OceanDNA-b31005/result_gtdb.tsv
[2023-03-16 23:07:08,354] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:07:08,356] [INFO] DFAST_QC result json was written to OceanDNA-b31005/dqc_result.json
[2023-03-16 23:07:08,356] [INFO] DFAST_QC completed!
[2023-03-16 23:07:08,356] [INFO] Total running time: 0h2m4s