[2024-01-24 13:09:34,008] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,018] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference
[2024-01-24 13:09:35,449] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,450] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,450] [INFO] Running command: gunzip -c /var/lib/cwl/stgf509a832-e199-4a35-9eb4-d2278bed4ef3/GCF_011044155.1_ASM1104415v1_genomic.fna.gz | prodigal -d GCF_011044155.1_ASM1104415v1_genomic.fna/cds.fna -a GCF_011044155.1_ASM1104415v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:47,740] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:47,740] [INFO] Task started: HMMsearch
[2024-01-24 13:09:47,741] [INFO] Running command: hmmsearch --tblout GCF_011044155.1_ASM1104415v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference/reference_markers.hmm GCF_011044155.1_ASM1104415v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:48,001] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:48,002] [INFO] Found 6/6 markers.
[2024-01-24 13:09:48,052] [INFO] Query marker FASTA was written to GCF_011044155.1_ASM1104415v1_genomic.fna/markers.fasta
[2024-01-24 13:09:48,052] [INFO] Task started: Blastn
[2024-01-24 13:09:48,053] [INFO] Running command: blastn -query GCF_011044155.1_ASM1104415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference/reference_markers.fasta -out GCF_011044155.1_ASM1104415v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:48,992] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:48,996] [INFO] Selected 24 target genomes.
[2024-01-24 13:09:48,996] [INFO] Target genome list was writen to GCF_011044155.1_ASM1104415v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:49,035] [INFO] Task started: fastANI
[2024-01-24 13:09:49,036] [INFO] Running command: fastANI --query /var/lib/cwl/stgf509a832-e199-4a35-9eb4-d2278bed4ef3/GCF_011044155.1_ASM1104415v1_genomic.fna.gz --refList GCF_011044155.1_ASM1104415v1_genomic.fna/target_genomes.txt --output GCF_011044155.1_ASM1104415v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:07,131] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:07,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:07,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:07,151] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:07,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:07,152] [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
Pikeienuella piscinae	strain=RR4-56	GCA_011044155.1	2748098	2748098	type	True	100.0	1455	1457	95	conclusive
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.5024	385	1457	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.2315	235	1457	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	77.1342	353	1457	95	below_threshold
Pontivivens ytuae	strain=MT2928	GCA_015679265.1	2789856	2789856	type	True	77.1214	279	1457	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.0667	288	1457	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	77.0543	200	1457	95	below_threshold
Meinhardsimonia xiamenensis	strain=DSM 24422	GCA_003001835.1	990712	990712	type	True	77.0274	245	1457	95	below_threshold
Meinhardsimonia xiamenensis	strain=CGMCC 1.10789	GCA_900102905.1	990712	990712	type	True	77.0225	244	1457	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	76.9341	401	1457	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	76.9267	269	1457	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	76.9232	401	1457	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.8778	375	1457	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.8672	227	1457	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	76.8584	267	1457	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	76.8327	362	1457	95	below_threshold
Rubrimonas cliftonensis	strain=DSM 15345	GCA_900107585.1	89524	89524	type	True	76.7987	397	1457	95	below_threshold
Roseovarius halotolerans	strain=CECT 8110	GCA_900172255.1	505353	505353	type	True	76.7984	213	1457	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	76.7802	215	1457	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	76.0099	215	1457	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	75.9954	141	1457	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.9742	156	1457	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.9344	216	1457	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	75.6187	194	1457	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:07,154] [INFO] DFAST Taxonomy check result was written to GCF_011044155.1_ASM1104415v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:07,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:07,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:07,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference/checkm_data
[2024-01-24 13:10:07,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:07,197] [INFO] Task started: CheckM
[2024-01-24 13:10:07,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011044155.1_ASM1104415v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011044155.1_ASM1104415v1_genomic.fna/checkm_input GCF_011044155.1_ASM1104415v1_genomic.fna/checkm_result
[2024-01-24 13:10:43,064] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:43,065] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:43,087] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:43,088] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:43,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011044155.1_ASM1104415v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:43,088] [INFO] Task started: Blastn
[2024-01-24 13:10:43,088] [INFO] Running command: blastn -query GCF_011044155.1_ASM1104415v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6995f04c-ad64-453c-9c29-7dbaeacd5ec9/dqc_reference/reference_markers_gtdb.fasta -out GCF_011044155.1_ASM1104415v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:44,673] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:44,677] [INFO] Selected 24 target genomes.
[2024-01-24 13:10:44,678] [INFO] Target genome list was writen to GCF_011044155.1_ASM1104415v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:44,711] [INFO] Task started: fastANI
[2024-01-24 13:10:44,711] [INFO] Running command: fastANI --query /var/lib/cwl/stgf509a832-e199-4a35-9eb4-d2278bed4ef3/GCF_011044155.1_ASM1104415v1_genomic.fna.gz --refList GCF_011044155.1_ASM1104415v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011044155.1_ASM1104415v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:01,457] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:01,475] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:01,476] [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_011044155.1	s__Pikeienuella piscinae	100.0	1455	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pikeienuella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011620265.1	s__Albidovulum sp011620265	77.5195	309	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	77.4722	389	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258405.1	s__Amaricoccus sp003258405	77.427	261	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	77.2463	238	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_005887635.2	s__Paroceanicella profunda	77.1565	350	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250135.1	s__SZUA-547 sp003250135	77.089	149	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-547	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102905.1	s__Meinhardsimonia xiamenensis	77.0225	244	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Meinhardsimonia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017995835.1	s__Amaricoccus sp017995835	77.0164	270	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695135.1	s__J013 sp003695135	76.9939	269	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__J013	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017993425.1	s__Amaricoccus sp017993425	76.9343	352	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113695.1	s__Albimonas pacifica	76.9287	403	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728195.1	s__Roseovarius indicus	76.9269	269	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	99.18	97.54	0.97	0.92	4	-
GCF_003448965.1	s__Paroceanicella sp003448965	76.9186	363	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	76.8869	220	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385685.1	s__Amaricoccus solimangrovi	76.8655	377	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	76.8513	372	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	76.8415	240	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	76.7918	366	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_007693835.1	s__Rubrimonas sp007693835	76.5697	307	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390865.1	s__HLUCCA09 sp003390865	76.5685	190	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871005.1	s__Acidimangrovimonas sediminis	76.442	280	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Acidimangrovimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	75.9954	141	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002291855.1	s__Sphingomonas_B sp002291855	75.5787	104	1457	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:01,477] [INFO] GTDB search result was written to GCF_011044155.1_ASM1104415v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:01,478] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:01,482] [INFO] DFAST_QC result json was written to GCF_011044155.1_ASM1104415v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:01,483] [INFO] DFAST_QC completed!
[2024-01-24 13:11:01,483] [INFO] Total running time: 0h1m27s