[2023-06-05 09:14:47,482] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:14:47,487] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:14:47,487] [INFO] DQC Reference Directory: /var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference
[2023-06-05 09:14:49,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:14:49,275] [INFO] Task started: Prodigal
[2023-06-05 09:14:49,276] [INFO] Running command: gunzip -c /var/lib/cwl/stg9882dffd-46bc-4dd9-8311-360eeee5e9ff/GCA_934539295.1_ERR7747324_bin.277_genomic.fna.gz | prodigal -d GCA_934539295.1_ERR7747324_bin.277_genomic.fna/cds.fna -a GCA_934539295.1_ERR7747324_bin.277_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:14:58,070] [INFO] Task succeeded: Prodigal
[2023-06-05 09:14:58,070] [INFO] Task started: HMMsearch
[2023-06-05 09:14:58,071] [INFO] Running command: hmmsearch --tblout GCA_934539295.1_ERR7747324_bin.277_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference/reference_markers.hmm GCA_934539295.1_ERR7747324_bin.277_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:14:58,318] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:14:58,320] [INFO] Found 6/6 markers.
[2023-06-05 09:14:58,356] [INFO] Query marker FASTA was written to GCA_934539295.1_ERR7747324_bin.277_genomic.fna/markers.fasta
[2023-06-05 09:14:58,356] [INFO] Task started: Blastn
[2023-06-05 09:14:58,357] [INFO] Running command: blastn -query GCA_934539295.1_ERR7747324_bin.277_genomic.fna/markers.fasta -db /var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference/reference_markers.fasta -out GCA_934539295.1_ERR7747324_bin.277_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:14:59,181] [INFO] Task succeeded: Blastn
[2023-06-05 09:14:59,186] [INFO] Selected 30 target genomes.
[2023-06-05 09:14:59,187] [INFO] Target genome list was writen to GCA_934539295.1_ERR7747324_bin.277_genomic.fna/target_genomes.txt
[2023-06-05 09:14:59,238] [INFO] Task started: fastANI
[2023-06-05 09:14:59,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg9882dffd-46bc-4dd9-8311-360eeee5e9ff/GCA_934539295.1_ERR7747324_bin.277_genomic.fna.gz --refList GCA_934539295.1_ERR7747324_bin.277_genomic.fna/target_genomes.txt --output GCA_934539295.1_ERR7747324_bin.277_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:15:17,979] [INFO] Task succeeded: fastANI
[2023-06-05 09:15:17,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:15:17,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:15:18,005] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:15:18,006] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:15:18,006] [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
Sphingosinicella humi	strain=QZX222	GCA_003129465.1	2068657	2068657	type	True	79.611	354	979	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	79.3083	396	979	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	78.8932	293	979	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.8677	321	979	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	78.8316	388	979	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	78.8175	321	979	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.7996	323	979	95	below_threshold
Sphingomonas astaxanthinifaciens	strain=DSM 22298	GCA_000711715.1	407019	407019	type	True	78.7742	270	979	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.6823	316	979	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.6796	330	979	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	78.6694	322	979	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	78.6575	297	979	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	78.6482	259	979	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.6379	247	979	95	below_threshold
Sphingomonas ginsengisoli An et al. 2013	strain=KACC 16858	GCA_009363895.1	363835	363835	type	True	78.5815	261	979	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.567	255	979	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.555	283	979	95	below_threshold
Sphingomonas spermidinifaciens	strain=9NM-10	GCA_002351485.1	1141889	1141889	type	True	78.4647	292	979	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.4565	261	979	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	78.3316	272	979	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.2259	282	979	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.2245	265	979	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.2243	297	979	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.1871	269	979	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	78.1733	252	979	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	78.1503	257	979	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	78.1304	260	979	95	below_threshold
Sphingomonas edaphi	strain=DAC4	GCA_003583725.1	2315689	2315689	type	True	77.9366	159	979	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	77.6773	180	979	95	below_threshold
Novosphingobium nitrogenifigens	strain=DSM 19370	GCA_000375445.1	378548	378548	type	True	77.4736	146	979	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:15:18,008] [INFO] DFAST Taxonomy check result was written to GCA_934539295.1_ERR7747324_bin.277_genomic.fna/tc_result.tsv
[2023-06-05 09:15:18,008] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:15:18,009] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:15:18,009] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference/checkm_data
[2023-06-05 09:15:18,010] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:15:18,046] [INFO] Task started: CheckM
[2023-06-05 09:15:18,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934539295.1_ERR7747324_bin.277_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934539295.1_ERR7747324_bin.277_genomic.fna/checkm_input GCA_934539295.1_ERR7747324_bin.277_genomic.fna/checkm_result
[2023-06-05 09:15:48,340] [INFO] Task succeeded: CheckM
[2023-06-05 09:15:48,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 9.26%
Strain heterogeneity: 16.67%
--------------------------------------------------------------------------------
[2023-06-05 09:15:48,367] [INFO] ===== Completeness check finished =====
[2023-06-05 09:15:48,367] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:15:48,367] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934539295.1_ERR7747324_bin.277_genomic.fna/markers.fasta)
[2023-06-05 09:15:48,368] [INFO] Task started: Blastn
[2023-06-05 09:15:48,368] [INFO] Running command: blastn -query GCA_934539295.1_ERR7747324_bin.277_genomic.fna/markers.fasta -db /var/lib/cwl/stg29ac6795-f69f-46bf-9918-3226ac270222/dqc_reference/reference_markers_gtdb.fasta -out GCA_934539295.1_ERR7747324_bin.277_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:15:49,674] [INFO] Task succeeded: Blastn
[2023-06-05 09:15:49,679] [INFO] Selected 24 target genomes.
[2023-06-05 09:15:49,679] [INFO] Target genome list was writen to GCA_934539295.1_ERR7747324_bin.277_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:15:50,011] [INFO] Task started: fastANI
[2023-06-05 09:15:50,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg9882dffd-46bc-4dd9-8311-360eeee5e9ff/GCA_934539295.1_ERR7747324_bin.277_genomic.fna.gz --refList GCA_934539295.1_ERR7747324_bin.277_genomic.fna/target_genomes_gtdb.txt --output GCA_934539295.1_ERR7747324_bin.277_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:16:04,912] [INFO] Task succeeded: fastANI
[2023-06-05 09:16:04,944] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 09:16:04,945] [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_003129465.1	s__Allosphingosinicella humi	79.6253	353	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	79.6016	315	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177405.1	s__Allosphingosinicella indica	79.5198	340	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012815.1	s__Allosphingosinicella vermicomposti	79.4568	310	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	79.2958	326	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	79.2835	398	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	78.9784	269	979	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_005882415.1	s__Allosphingosinicella sp005882415	78.9758	296	979	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	78.9538	331	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	99.90	99.89	0.98	0.97	3	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	78.9198	247	979	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_004135585.1	s__Allosphingosinicella sp004135585	78.9071	379	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	78.8181	320	979	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_018863195.1	s__XMGL2 sp018863195	78.8097	279	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995055.1	s__Allosphingosinicella ginsenosidimutans	78.7862	324	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239415.1	s__Allosphingosinicella sp019239415	78.7337	328	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	78.7304	355	979	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	78.7126	314	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	78.681	330	979	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_011927725.1	s__Sphingomicrobium kaistense	78.6482	259	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	78.4171	264	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	78.1948	218	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151485.1	s__Allosphingosinicella sp004151485	78.1468	314	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241465.1	s__Sphingomonas echinoides	78.1161	261	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_003583725.1	s__Sphingomicrobium edaphi	77.9366	159	979	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:16:04,947] [INFO] GTDB search result was written to GCA_934539295.1_ERR7747324_bin.277_genomic.fna/result_gtdb.tsv
[2023-06-05 09:16:04,947] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:16:04,952] [INFO] DFAST_QC result json was written to GCA_934539295.1_ERR7747324_bin.277_genomic.fna/dqc_result.json
[2023-06-05 09:16:04,952] [INFO] DFAST_QC completed!
[2023-06-05 09:16:04,952] [INFO] Total running time: 0h1m17s