[2024-01-24 12:07:06,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,760] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference
[2024-01-24 12:07:07,971] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,972] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,972] [INFO] Running command: gunzip -c /var/lib/cwl/stg295e7f48-440f-4cba-8745-7d361ee2618a/GCF_024158125.1_ASM2415812v1_genomic.fna.gz | prodigal -d GCF_024158125.1_ASM2415812v1_genomic.fna/cds.fna -a GCF_024158125.1_ASM2415812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:17,961] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:17,961] [INFO] Task started: HMMsearch
[2024-01-24 12:07:17,962] [INFO] Running command: hmmsearch --tblout GCF_024158125.1_ASM2415812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference/reference_markers.hmm GCF_024158125.1_ASM2415812v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:18,266] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:18,267] [INFO] Found 6/6 markers.
[2024-01-24 12:07:18,302] [INFO] Query marker FASTA was written to GCF_024158125.1_ASM2415812v1_genomic.fna/markers.fasta
[2024-01-24 12:07:18,303] [INFO] Task started: Blastn
[2024-01-24 12:07:18,303] [INFO] Running command: blastn -query GCF_024158125.1_ASM2415812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference/reference_markers.fasta -out GCF_024158125.1_ASM2415812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:19,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:19,317] [INFO] Selected 31 target genomes.
[2024-01-24 12:07:19,317] [INFO] Target genome list was writen to GCF_024158125.1_ASM2415812v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:19,328] [INFO] Task started: fastANI
[2024-01-24 12:07:19,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg295e7f48-440f-4cba-8745-7d361ee2618a/GCF_024158125.1_ASM2415812v1_genomic.fna.gz --refList GCF_024158125.1_ASM2415812v1_genomic.fna/target_genomes.txt --output GCF_024158125.1_ASM2415812v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:45,268] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:45,269] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:45,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:45,295] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:07:45,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:07:45,296] [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
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.6627	240	1129	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	77.6065	285	1129	95	below_threshold
Kaustia mangrovi	strain=R1DC25	GCA_015482775.1	2593653	2593653	type	True	77.5051	291	1129	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	77.4906	217	1129	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	77.4028	304	1129	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	77.3038	258	1129	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	77.2894	252	1129	95	below_threshold
Propylenella binzhouense	strain=L72	GCA_009866965.1	2555902	2555902	type	True	77.2447	226	1129	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	77.0753	234	1129	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	77.0503	238	1129	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	77.043	205	1129	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	77.0371	268	1129	95	below_threshold
Methylobacterium nodulans	strain=ORS 2060	GCA_000022085.1	114616	114616	type	True	76.9847	247	1129	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.972	258	1129	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.9653	268	1129	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.9527	243	1129	95	below_threshold
Methylobacterium radiotolerans	strain=JCM 2831	GCA_000019725.1	31998	31998	type	True	76.9053	220	1129	95	below_threshold
Albimonas pacifica	strain=CGMCC 1.11030	GCA_900113695.1	1114924	1114924	type	True	76.885	336	1129	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	76.8758	255	1129	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.8626	286	1129	95	below_threshold
Aureimonas endophytica	strain=CGMCC 1.15367	GCA_014642635.1	2027858	2027858	type	True	76.8267	225	1129	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.7879	278	1129	95	below_threshold
Methylobacterium radiotolerans	strain=NBRC 15690	GCA_007991055.1	31998	31998	type	True	76.7817	219	1129	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.7754	145	1129	95	below_threshold
Methylobacterium crusticola	strain=MIMD6	GCA_003574465.1	1697972	1697972	type	True	76.7374	278	1129	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.7172	284	1129	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.7072	164	1129	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	76.7007	226	1129	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6687	290	1129	95	below_threshold
Hyphomicrobium sulfonivorans	strain=S1	GCA_013306565.1	121290	121290	type	True	76.5982	91	1129	95	below_threshold
Methylobacterium aquaticum	strain=DSM 16371	GCA_001043915.1	270351	270351	type	True	76.5913	258	1129	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:45,297] [INFO] DFAST Taxonomy check result was written to GCF_024158125.1_ASM2415812v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:45,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:45,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:45,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference/checkm_data
[2024-01-24 12:07:45,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:45,333] [INFO] Task started: CheckM
[2024-01-24 12:07:45,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024158125.1_ASM2415812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024158125.1_ASM2415812v1_genomic.fna/checkm_input GCF_024158125.1_ASM2415812v1_genomic.fna/checkm_result
[2024-01-24 12:08:21,579] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:21,581] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:21,608] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:21,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:21,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024158125.1_ASM2415812v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:21,609] [INFO] Task started: Blastn
[2024-01-24 12:08:21,609] [INFO] Running command: blastn -query GCF_024158125.1_ASM2415812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5ed3f3ae-74ce-45f5-ac03-cf33da7482f8/dqc_reference/reference_markers_gtdb.fasta -out GCF_024158125.1_ASM2415812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:23,541] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:23,545] [INFO] Selected 35 target genomes.
[2024-01-24 12:08:23,546] [INFO] Target genome list was writen to GCF_024158125.1_ASM2415812v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:23,572] [INFO] Task started: fastANI
[2024-01-24 12:08:23,572] [INFO] Running command: fastANI --query /var/lib/cwl/stg295e7f48-440f-4cba-8745-7d361ee2618a/GCF_024158125.1_ASM2415812v1_genomic.fna.gz --refList GCF_024158125.1_ASM2415812v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024158125.1_ASM2415812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:51,630] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:51,661] [INFO] Found 35 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:08:51,661] [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_014196925.1	s__Chelatococcus_A caeni	77.607	285	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_015482775.1	s__Kaustia mangrovi	77.4949	292	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Kaustia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	77.4765	218	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866965.1	s__Propylenella binzhouense	77.2447	226	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003105195.1	s__FEB-22 sp003105195	77.1613	233	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__FEB-22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699855.1	s__GCA-016699855 sp016699855	77.1581	282	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__GCA-016699855	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013389075.1	s__JACAEB01 sp013389075	77.0893	167	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JACAEB01;f__JACAEB01;g__JACAEB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386575.1	s__BN140002 sp008386575	77.0747	234	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__BN140002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009697225.1	s__Halovulum marinum	77.0476	268	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407205.1	s__Cereibacter_A sp002407205	77.0454	211	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	77.0433	205	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173735.1	s__Methylobacterium radiodurans	76.9946	240	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022085.1	s__Methylobacterium nodulans	76.9945	247	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	76.966	268	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	76.9176	240	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	76.9147	236	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902141855.1	s__Methylobacterium dankookense	76.9043	265	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173775.1	s__Methylobacterium sp003173775	76.8948	279	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	95.16	95.16	0.87	0.87	2	-
GCF_004745635.1	s__Methylobacterium sp004745635	76.8726	285	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280485.1	s__NCED01 sp002280485	76.8628	132	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__NCED01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003058325.1	s__Methylobacterium currus	76.8562	266	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642695.1	s__Parvibaculum sp017642695	76.8258	184	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	99.96	99.92	0.99	0.97	4	-
GCF_014642635.1	s__Aureimonas_A endophytica	76.8167	226	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644455.1	s__Caldovatus sediminis	76.7844	271	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Caldovatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110915.1	s__Propylenella sp900110915	76.7838	181	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003574465.1	s__Methylobacterium crusticola	76.7608	275	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	76.7437	190	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008039615.1	s__SYSU-D60007 sp008039615	76.7121	289	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__SYSU-D60007	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005281615.1	s__Rhodoligotrophos sp005281615	76.6936	165	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Im1;g__Rhodoligotrophos	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002928395.1	s__Hyphomicrobium sp002928395	76.6899	69	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Hyphomicrobiaceae;g__Hyphomicrobium	95.0	100.00	100.00	0.99	0.99	2	-
GCA_007693835.1	s__Rubrimonas sp007693835	76.6501	228	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916275.1	s__Rubellimicrobium sp017916275	76.6241	166	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rubellimicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001043915.1	s__Methylobacterium aquaticum	76.5916	258	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247715.1	s__Palsa-881 sp019247715	76.2539	139	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Palsa-881	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002595.1	s__JABDJG01 sp013002595	75.7203	71	1129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Aestuariivirgaceae;g__JABDJG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:51,663] [INFO] GTDB search result was written to GCF_024158125.1_ASM2415812v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:51,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:51,670] [INFO] DFAST_QC result json was written to GCF_024158125.1_ASM2415812v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:51,671] [INFO] DFAST_QC completed!
[2024-01-24 12:08:51,671] [INFO] Total running time: 0h1m45s