[2023-03-18 10:41:19,252] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:41:19,253] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:41:19,253] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference
[2023-03-18 10:41:20,434] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:41:20,435] [INFO] Task started: Prodigal
[2023-03-18 10:41:20,435] [INFO] Running command: cat /var/lib/cwl/stgd5b70ed2-62e7-480a-8104-0505649f7e65/OceanDNA-b31547.fa | prodigal -d OceanDNA-b31547/cds.fna -a OceanDNA-b31547/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:41:38,928] [INFO] Task succeeded: Prodigal
[2023-03-18 10:41:38,928] [INFO] Task started: HMMsearch
[2023-03-18 10:41:38,928] [INFO] Running command: hmmsearch --tblout OceanDNA-b31547/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference/reference_markers.hmm OceanDNA-b31547/protein.faa > /dev/null
[2023-03-18 10:41:39,132] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:41:39,133] [INFO] Found 6/6 markers.
[2023-03-18 10:41:39,157] [INFO] Query marker FASTA was written to OceanDNA-b31547/markers.fasta
[2023-03-18 10:41:39,158] [INFO] Task started: Blastn
[2023-03-18 10:41:39,158] [INFO] Running command: blastn -query OceanDNA-b31547/markers.fasta -db /var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference/reference_markers.fasta -out OceanDNA-b31547/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:41:39,913] [INFO] Task succeeded: Blastn
[2023-03-18 10:41:39,914] [INFO] Selected 31 target genomes.
[2023-03-18 10:41:39,915] [INFO] Target genome list was writen to OceanDNA-b31547/target_genomes.txt
[2023-03-18 10:41:39,933] [INFO] Task started: fastANI
[2023-03-18 10:41:39,933] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b70ed2-62e7-480a-8104-0505649f7e65/OceanDNA-b31547.fa --refList OceanDNA-b31547/target_genomes.txt --output OceanDNA-b31547/fastani_result.tsv --threads 1
[2023-03-18 10:42:00,883] [INFO] Task succeeded: fastANI
[2023-03-18 10:42:00,884] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:42:00,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:42:00,900] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:42:00,901] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:42:00,901] [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
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	79.2163	307	1001	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	78.3826	283	1001	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.3747	320	1001	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.2451	295	1001	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	78.2182	282	1001	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.0859	268	1001	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.0849	277	1001	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	77.9957	274	1001	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	77.9131	266	1001	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	77.8902	240	1001	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.8699	219	1001	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	77.7572	254	1001	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	77.7147	215	1001	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	77.6474	214	1001	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	77.616	192	1001	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.6002	303	1001	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	77.5797	202	1001	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.5343	230	1001	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.5052	223	1001	95	below_threshold
Sphingomonas prati	strain=CGMCC 1.15645	GCA_014643515.1	1843237	1843237	type	True	77.4892	198	1001	95	below_threshold
Sphingomonas prati	strain=W18RD	GCA_009755805.1	1843237	1843237	type	True	77.4507	201	1001	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	77.4435	200	1001	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.4119	242	1001	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.3847	212	1001	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	77.377	205	1001	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	77.3029	197	1001	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	77.2382	195	1001	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	77.232	120	1001	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	77.2263	209	1001	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	77.1554	217	1001	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	76.8385	108	1001	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:42:00,902] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31547/tc_result.tsv
[2023-03-18 10:42:00,903] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:42:00,904] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:42:00,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference/checkm_data
[2023-03-18 10:42:00,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:42:00,911] [INFO] Task started: CheckM
[2023-03-18 10:42:00,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31547/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31547/checkm_input OceanDNA-b31547/checkm_result
[2023-03-18 10:42:48,268] [INFO] Task succeeded: CheckM
[2023-03-18 10:42:48,268] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:42:48,271] [INFO] ===== Completeness check finished =====
[2023-03-18 10:42:48,271] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:42:48,271] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31547/markers.fasta)
[2023-03-18 10:42:48,272] [INFO] Task started: Blastn
[2023-03-18 10:42:48,272] [INFO] Running command: blastn -query OceanDNA-b31547/markers.fasta -db /var/lib/cwl/stgbb13a80e-62ec-4075-9511-c9d788a3539e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31547/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:42:49,868] [INFO] Task succeeded: Blastn
[2023-03-18 10:42:49,869] [INFO] Selected 34 target genomes.
[2023-03-18 10:42:49,869] [INFO] Target genome list was writen to OceanDNA-b31547/target_genomes_gtdb.txt
[2023-03-18 10:42:49,908] [INFO] Task started: fastANI
[2023-03-18 10:42:49,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5b70ed2-62e7-480a-8104-0505649f7e65/OceanDNA-b31547.fa --refList OceanDNA-b31547/target_genomes_gtdb.txt --output OceanDNA-b31547/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:43:12,521] [INFO] Task succeeded: fastANI
[2023-03-18 10:43:12,539] [INFO] Found 34 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:43:12,539] [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
GCF_002355275.1	s__Rhizorhabdus dicambivorans	79.1781	310	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCF_001429065.1	s__Rhizorhabdus sp001429065	78.8357	301	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.3869	319	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	78.2573	294	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_009755815.1	s__Sphingomonas_M formosensis	78.0849	277	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	78.0746	239	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153545.1	s__Sphingobium sp000153545	78.0408	180	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	-
GCF_008274695.1	s__Rhizorhabdus montanisoli	78.0392	289	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	77.954	195	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590775.1	s__Sphingobium_A sp003590775	77.9182	238	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005518185.1	s__Chakrabartia godavariana	77.9008	179	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	77.8506	206	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333335.1	s__Sphingomonas_N sp000333335	77.8404	193	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	77.8265	168	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	77.7806	220	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	77.7612	253	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	77.7072	210	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000445105.1	s__Sphingobium lactosutens	77.7047	215	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	77.683	192	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	77.6779	240	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	77.6422	219	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	77.6041	233	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	77.6002	303	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	77.5471	229	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002281485.1	s__Sphingomonas sp002281485	77.533	168	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	77.5147	242	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016937575.1	s__Sphingomonas aeriglobus	77.4982	194	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643515.1	s__Sphingomonas_G prati	77.4741	199	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	100.00	100.00	1.00	1.00	3	-
GCF_014197105.1	s__Sphingomonas jinjuensis	77.3796	204	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012735.1	s__Allosphingosinicella deserti	77.2247	210	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344055.1	s__Allosphingosinicella sp002344055	77.2155	173	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005883305.1	s__Allosphingosinicella sp005883305	77.134	175	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005882415.1	s__Allosphingosinicella sp005882415	77.005	131	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002953135.1	s__Sphingobium sp002953135	76.8528	159	1001	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:43:12,540] [INFO] GTDB search result was written to OceanDNA-b31547/result_gtdb.tsv
[2023-03-18 10:43:12,542] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:43:12,545] [INFO] DFAST_QC result json was written to OceanDNA-b31547/dqc_result.json
[2023-03-18 10:43:12,545] [INFO] DFAST_QC completed!
[2023-03-18 10:43:12,545] [INFO] Total running time: 0h1m53s