[2023-03-18 22:08:46,355] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:08:46,356] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:08:46,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference
[2023-03-18 22:08:47,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:08:47,463] [INFO] Task started: Prodigal
[2023-03-18 22:08:47,463] [INFO] Running command: cat /var/lib/cwl/stgf840f94a-5a5d-4fc1-bb84-7d6ab4c1a23e/OceanDNA-b32039.fa | prodigal -d OceanDNA-b32039/cds.fna -a OceanDNA-b32039/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:09:06,351] [INFO] Task succeeded: Prodigal
[2023-03-18 22:09:06,352] [INFO] Task started: HMMsearch
[2023-03-18 22:09:06,352] [INFO] Running command: hmmsearch --tblout OceanDNA-b32039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference/reference_markers.hmm OceanDNA-b32039/protein.faa > /dev/null
[2023-03-18 22:09:06,542] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:09:06,542] [INFO] Found 6/6 markers.
[2023-03-18 22:09:06,564] [INFO] Query marker FASTA was written to OceanDNA-b32039/markers.fasta
[2023-03-18 22:09:06,565] [INFO] Task started: Blastn
[2023-03-18 22:09:06,565] [INFO] Running command: blastn -query OceanDNA-b32039/markers.fasta -db /var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference/reference_markers.fasta -out OceanDNA-b32039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:09:07,445] [INFO] Task succeeded: Blastn
[2023-03-18 22:09:07,445] [INFO] Selected 30 target genomes.
[2023-03-18 22:09:07,446] [INFO] Target genome list was writen to OceanDNA-b32039/target_genomes.txt
[2023-03-18 22:09:07,470] [INFO] Task started: fastANI
[2023-03-18 22:09:07,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgf840f94a-5a5d-4fc1-bb84-7d6ab4c1a23e/OceanDNA-b32039.fa --refList OceanDNA-b32039/target_genomes.txt --output OceanDNA-b32039/fastani_result.tsv --threads 1
[2023-03-18 22:09:26,630] [INFO] Task succeeded: fastANI
[2023-03-18 22:09:26,631] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:09:26,631] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:09:26,647] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:09:26,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:09:26,647] [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
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.2158	336	1017	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.093	326	1017	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.0687	372	1017	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.037	303	1017	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	77.9459	271	1017	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	77.9336	272	1017	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	77.7444	254	1017	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	77.7376	297	1017	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.6987	303	1017	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	77.6762	265	1017	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.6431	395	1017	95	below_threshold
Sphingomonas jejuensis	strain=DSM 27651	GCA_011927695.1	904715	904715	type	True	77.593	241	1017	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	77.5308	278	1017	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.4529	242	1017	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	77.4082	305	1017	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	77.3781	289	1017	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	77.3377	270	1017	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	77.2544	200	1017	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	77.249	247	1017	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	77.2406	304	1017	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.2269	233	1017	95	below_threshold
Sphingomonas prati	strain=CGMCC 1.15645	GCA_014643515.1	1843237	1843237	type	True	77.2142	250	1017	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.1692	261	1017	95	below_threshold
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	77.1445	203	1017	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	76.9508	235	1017	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	76.8452	181	1017	95	below_threshold
Sphingomonas arenae	strain=SYSU D00720	GCA_016924655.1	2812555	2812555	type	True	76.8	144	1017	95	below_threshold
Bradyrhizobium archetypum	strain=WSM 1744	GCA_013114835.1	2721160	2721160	type	True	75.1658	76	1017	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	74.6528	57	1017	95	below_threshold
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	74.6528	57	1017	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:09:26,648] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32039/tc_result.tsv
[2023-03-18 22:09:26,648] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:09:26,648] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:09:26,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference/checkm_data
[2023-03-18 22:09:26,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:09:26,721] [INFO] Task started: CheckM
[2023-03-18 22:09:26,721] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32039/checkm_input OceanDNA-b32039/checkm_result
[2023-03-18 22:10:14,419] [INFO] Task succeeded: CheckM
[2023-03-18 22:10:14,419] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 63.54%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 22:10:14,455] [INFO] ===== Completeness check finished =====
[2023-03-18 22:10:14,455] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:10:14,455] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32039/markers.fasta)
[2023-03-18 22:10:14,456] [INFO] Task started: Blastn
[2023-03-18 22:10:14,457] [INFO] Running command: blastn -query OceanDNA-b32039/markers.fasta -db /var/lib/cwl/stgd1795b25-c094-4f8d-bfbb-ce7022261d61/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:10:16,173] [INFO] Task succeeded: Blastn
[2023-03-18 22:10:16,174] [INFO] Selected 32 target genomes.
[2023-03-18 22:10:16,174] [INFO] Target genome list was writen to OceanDNA-b32039/target_genomes_gtdb.txt
[2023-03-18 22:10:16,209] [INFO] Task started: fastANI
[2023-03-18 22:10:16,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgf840f94a-5a5d-4fc1-bb84-7d6ab4c1a23e/OceanDNA-b32039.fa --refList OceanDNA-b32039/target_genomes_gtdb.txt --output OceanDNA-b32039/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:10:36,484] [INFO] Task succeeded: fastANI
[2023-03-18 22:10:36,501] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:10:36,501] [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_013113735.1	s__Sphingomonas_I sp013113735	78.2382	354	1017	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_900113315.1	s__Sphingomonas_G jatrophae	78.2158	336	1017	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_903644055.1	s__Sphingomonas_I sp903644055	78.13	215	1017	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_003034225.1	s__Sphingomonas_E fennica	78.1037	326	1017	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_003391115.1	s__Sphingomonas_I crusticola	78.037	303	1017	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_003050615.1	s__Sphingomonas_H oleivorans	77.8605	286	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248515.1	s__Sphingomonas_I sp003248515	77.7804	304	1017	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_900188165.1	s__Sphingomonas_E laterariae	77.7443	254	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333335.1	s__Sphingomonas_N sp000333335	77.7261	267	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785815.1	s__Sphingomonas_G solaris	77.7241	295	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724715.1	s__SCN-67-18 sp001724715	77.6509	245	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	77.5421	277	1017	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	77.4756	212	1017	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_002127225.1	s__Sphingomonas sp002127225	77.4464	261	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	77.3803	288	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	77.3445	288	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
GCF_011761945.1	s__Sphingomonas leidyi	77.3369	270	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	77.2502	231	1017	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_000974765.1	s__Sphingomonas_B changbaiensis	77.2401	201	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	77.2113	176	1017	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_009753715.1	s__Sphingomonas_B horti	77.1823	262	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003129465.1	s__Allosphingosinicella humi	77.1445	203	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232625.1	s__Allosphingosinicella sp019232625	77.0047	215	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCF_004564275.1	s__Allosphingosinicella parva	77.0034	229	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873375.1	s__Sphingomicrobium sp014873375	76.8184	117	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016924655.1	s__Sphingomicrobium sp016924655	76.8135	143	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	76.6977	227	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812805.1	s__Sphingomicrobium sp013812805	76.57	93	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000359125.1	s__Mesorhizobium sp000359125	75.5622	88	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331955.1	s__Roseitalea porphyridii	75.2786	73	1017	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:10:36,503] [INFO] GTDB search result was written to OceanDNA-b32039/result_gtdb.tsv
[2023-03-18 22:10:36,504] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:10:36,510] [INFO] DFAST_QC result json was written to OceanDNA-b32039/dqc_result.json
[2023-03-18 22:10:36,510] [INFO] DFAST_QC completed!
[2023-03-18 22:10:36,510] [INFO] Total running time: 0h1m50s