[2024-01-24 13:40:28,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,691] [INFO] DQC Reference Directory: /var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference
[2024-01-24 13:40:31,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,144] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,144] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd2314ff-f45b-45cf-a540-16947ecd7ddf/GCF_028607085.1_ASM2860708v1_genomic.fna.gz | prodigal -d GCF_028607085.1_ASM2860708v1_genomic.fna/cds.fna -a GCF_028607085.1_ASM2860708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:43,751] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:43,751] [INFO] Task started: HMMsearch
[2024-01-24 13:40:43,751] [INFO] Running command: hmmsearch --tblout GCF_028607085.1_ASM2860708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference/reference_markers.hmm GCF_028607085.1_ASM2860708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:44,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:44,087] [INFO] Found 6/6 markers.
[2024-01-24 13:40:44,349] [INFO] Query marker FASTA was written to GCF_028607085.1_ASM2860708v1_genomic.fna/markers.fasta
[2024-01-24 13:40:44,371] [INFO] Task started: Blastn
[2024-01-24 13:40:44,371] [INFO] Running command: blastn -query GCF_028607085.1_ASM2860708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference/reference_markers.fasta -out GCF_028607085.1_ASM2860708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:45,289] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:45,292] [INFO] Selected 26 target genomes.
[2024-01-24 13:40:45,293] [INFO] Target genome list was writen to GCF_028607085.1_ASM2860708v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:45,309] [INFO] Task started: fastANI
[2024-01-24 13:40:45,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd2314ff-f45b-45cf-a540-16947ecd7ddf/GCF_028607085.1_ASM2860708v1_genomic.fna.gz --refList GCF_028607085.1_ASM2860708v1_genomic.fna/target_genomes.txt --output GCF_028607085.1_ASM2860708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:07,818] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:07,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:07,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:07,840] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:07,840] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:07,841] [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 solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	80.2621	549	1434	95	below_threshold
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	80.2073	556	1434	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	80.0871	566	1434	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.9967	519	1434	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.9331	551	1434	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	79.853	516	1434	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	79.6057	579	1434	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	79.6016	518	1434	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	79.5412	530	1434	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	79.5003	466	1434	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.4653	494	1434	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	79.3317	401	1434	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	79.1044	446	1434	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	79.096	533	1434	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.0688	427	1434	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.0628	428	1434	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.9648	420	1434	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.9102	512	1434	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.9101	399	1434	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	78.9085	464	1434	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	78.8329	490	1434	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	78.8071	498	1434	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.7655	406	1434	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	78.7618	483	1434	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	78.6125	483	1434	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	74.9072	76	1434	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:07,843] [INFO] DFAST Taxonomy check result was written to GCF_028607085.1_ASM2860708v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:07,843] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:07,844] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:07,844] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference/checkm_data
[2024-01-24 13:41:07,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:07,891] [INFO] Task started: CheckM
[2024-01-24 13:41:07,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028607085.1_ASM2860708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028607085.1_ASM2860708v1_genomic.fna/checkm_input GCF_028607085.1_ASM2860708v1_genomic.fna/checkm_result
[2024-01-24 13:41:49,080] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:49,082] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:49,105] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:49,105] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:49,106] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028607085.1_ASM2860708v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:49,106] [INFO] Task started: Blastn
[2024-01-24 13:41:49,107] [INFO] Running command: blastn -query GCF_028607085.1_ASM2860708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdda14f11-ac7d-4541-9f17-215fb04a4af7/dqc_reference/reference_markers_gtdb.fasta -out GCF_028607085.1_ASM2860708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:50,666] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:50,671] [INFO] Selected 26 target genomes.
[2024-01-24 13:41:50,671] [INFO] Target genome list was writen to GCF_028607085.1_ASM2860708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:50,709] [INFO] Task started: fastANI
[2024-01-24 13:41:50,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd2314ff-f45b-45cf-a540-16947ecd7ddf/GCF_028607085.1_ASM2860708v1_genomic.fna.gz --refList GCF_028607085.1_ASM2860708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028607085.1_ASM2860708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:12,438] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:12,458] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:12,458] [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	80.4518	607	1434	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_007785815.1	s__Sphingomonas_G solaris	80.2899	546	1434	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_009739515.1	s__Sphingomonas_G sp009739515	80.1409	562	1434	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_000016765.1	s__Rhizorhabdus wittichii	80.1311	631	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.9924	520	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	79.8376	363	1434	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_013778325.1	s__Sphingomonas_N chungangi	79.6374	513	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	79.596	578	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCA_000333335.1	s__Sphingomonas_N sp000333335	79.5838	422	1434	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_001428605.1	s__Rhizorhabdus sp001428605	79.5759	574	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.98	99.98	0.99	0.99	3	-
GCF_001015195.1	s__Rhizorhabdus sp001015195	79.5693	520	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761305.1	s__Sphingomonas_I vulcanisoli	79.4942	465	1434	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	79.4601	494	1434	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_903871605.1	s__Sphingomonas_N sp903871605	79.4501	503	1434	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_018863195.1	s__XMGL2 sp018863195	79.3842	487	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003391115.1	s__Sphingomonas_I crusticola	79.3252	401	1434	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_000226955.1	s__Sphingomonas elodea_A	79.0958	465	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.074	426	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900177405.1	s__Allosphingosinicella indica	79.0263	389	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101455.1	s__Rhizorhabdus sp900101455	78.9107	419	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	78.8038	480	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014204695.1	s__Sphingomonas sp001897045	78.7966	520	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	78.7945	493	1434	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	78.7087	412	1434	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_007859935.1	s__Posidoniimonas polymericola	74.9072	76	1434	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Posidoniimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,460] [INFO] GTDB search result was written to GCF_028607085.1_ASM2860708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:12,461] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:12,470] [INFO] DFAST_QC result json was written to GCF_028607085.1_ASM2860708v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:12,470] [INFO] DFAST_QC completed!
[2024-01-24 13:42:12,470] [INFO] Total running time: 0h1m44s