[2024-01-24 12:51:04,638] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:04,640] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:04,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference
[2024-01-24 12:51:05,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:05,840] [INFO] Task started: Prodigal
[2024-01-24 12:51:05,841] [INFO] Running command: gunzip -c /var/lib/cwl/stg2766d51f-a68a-44ad-9a8b-fb34024ed495/GCF_003675895.1_ASM367589v1_genomic.fna.gz | prodigal -d GCF_003675895.1_ASM367589v1_genomic.fna/cds.fna -a GCF_003675895.1_ASM367589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:15,310] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:15,311] [INFO] Task started: HMMsearch
[2024-01-24 12:51:15,311] [INFO] Running command: hmmsearch --tblout GCF_003675895.1_ASM367589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference/reference_markers.hmm GCF_003675895.1_ASM367589v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:15,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:15,610] [INFO] Found 6/6 markers.
[2024-01-24 12:51:15,661] [INFO] Query marker FASTA was written to GCF_003675895.1_ASM367589v1_genomic.fna/markers.fasta
[2024-01-24 12:51:15,661] [INFO] Task started: Blastn
[2024-01-24 12:51:15,662] [INFO] Running command: blastn -query GCF_003675895.1_ASM367589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference/reference_markers.fasta -out GCF_003675895.1_ASM367589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:16,451] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:16,456] [INFO] Selected 20 target genomes.
[2024-01-24 12:51:16,456] [INFO] Target genome list was writen to GCF_003675895.1_ASM367589v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:16,470] [INFO] Task started: fastANI
[2024-01-24 12:51:16,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg2766d51f-a68a-44ad-9a8b-fb34024ed495/GCF_003675895.1_ASM367589v1_genomic.fna.gz --refList GCF_003675895.1_ASM367589v1_genomic.fna/target_genomes.txt --output GCF_003675895.1_ASM367589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:33,464] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:33,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:33,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:33,484] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:33,484] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:33,484] [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
Parashewanella curva	strain=C51	GCA_003675895.1	2338552	2338552	type	True	100.0	1479	1491	95	conclusive
Parashewanella tropica	strain=MEBiC05444	GCA_004358445.1	2547970	2547970	type	True	83.9094	857	1491	95	below_threshold
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	78.6306	285	1491	95	below_threshold
Shewanella pealeana	strain=ATCC 700345	GCA_000018285.1	70864	70864	type	True	78.3992	134	1491	95	below_threshold
Shewanella japonica	strain=KCTC 22435	GCA_002075795.1	93973	93973	type	True	78.269	154	1491	95	below_threshold
Shewanella sairae	strain=JCM 11563	GCA_019655015.1	190310	190310	type	True	78.2655	148	1491	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	78.1185	139	1491	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.0733	131	1491	95	below_threshold
Shewanella marina	strain=JCM 15074	GCA_000614975.1	487319	487319	type	True	78.0565	130	1491	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	78.017	145	1491	95	below_threshold
Shewanella maritima	strain=D4-2	GCA_004295345.1	2520507	2520507	type	True	77.989	178	1491	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	77.964	142	1491	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	77.9583	125	1491	95	below_threshold
Parashewanella spongiae	strain=HJ039	GCA_004358345.1	342950	342950	type	True	77.9065	266	1491	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	77.8851	148	1491	95	below_threshold
Parashewanella spongiae	strain=KCTC 22492	GCA_003676335.1	342950	342950	type	True	77.8141	254	1491	95	below_threshold
Parashewanella spongiae	strain=KCTC 22492	GCA_023283745.1	342950	342950	type	True	77.8011	250	1491	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	77.4618	125	1491	95	below_threshold
Shewanella surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	77.3897	112	1491	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.5366	57	1491	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:33,486] [INFO] DFAST Taxonomy check result was written to GCF_003675895.1_ASM367589v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:33,486] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:33,486] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:33,486] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference/checkm_data
[2024-01-24 12:51:33,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:33,537] [INFO] Task started: CheckM
[2024-01-24 12:51:33,538] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003675895.1_ASM367589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003675895.1_ASM367589v1_genomic.fna/checkm_input GCF_003675895.1_ASM367589v1_genomic.fna/checkm_result
[2024-01-24 12:52:07,039] [INFO] Task succeeded: CheckM
[2024-01-24 12:52:07,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:52:07,062] [INFO] ===== Completeness check finished =====
[2024-01-24 12:52:07,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:52:07,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003675895.1_ASM367589v1_genomic.fna/markers.fasta)
[2024-01-24 12:52:07,063] [INFO] Task started: Blastn
[2024-01-24 12:52:07,063] [INFO] Running command: blastn -query GCF_003675895.1_ASM367589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90904939-7c28-4ce9-b98a-5816c7684c52/dqc_reference/reference_markers_gtdb.fasta -out GCF_003675895.1_ASM367589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:08,190] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:08,194] [INFO] Selected 15 target genomes.
[2024-01-24 12:52:08,194] [INFO] Target genome list was writen to GCF_003675895.1_ASM367589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:08,229] [INFO] Task started: fastANI
[2024-01-24 12:52:08,230] [INFO] Running command: fastANI --query /var/lib/cwl/stg2766d51f-a68a-44ad-9a8b-fb34024ed495/GCF_003675895.1_ASM367589v1_genomic.fna.gz --refList GCF_003675895.1_ASM367589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003675895.1_ASM367589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:21,602] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:21,621] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:21,622] [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_003675895.1	s__Parashewanella curva	100.0	1480	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004358445.1	s__Parashewanella tropica	83.8956	862	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900895.1	s__Parashewanella sp016900895	78.6044	288	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168585.1	s__Parashewanella sp004168585	78.5919	268	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	78.375	136	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002075795.1	s__Shewanella japonica	78.285	154	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.37	97.91	0.95	0.93	6	-
GCF_014648035.1	s__Shewanella algicola	78.1187	139	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_000614975.1	s__Shewanella marina	78.1016	130	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011765625.1	s__Shewanella aestuarii_A	77.9883	148	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007567505.1	s__Shewanella donghaensis	77.964	142	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358345.1	s__Parashewanella spongiae	77.8828	271	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001957125.1	s__Shewanella sp001957125	77.8482	126	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002873615.1	s__Shewanella sp002873615	77.7385	156	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855395.1	s__Shewanella livingstonensis	77.7118	144	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009663145.1	s__Shewanella sp009663145	77.4568	166	1491	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:21,624] [INFO] GTDB search result was written to GCF_003675895.1_ASM367589v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:21,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:21,629] [INFO] DFAST_QC result json was written to GCF_003675895.1_ASM367589v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:21,629] [INFO] DFAST_QC completed!
[2024-01-24 12:52:21,629] [INFO] Total running time: 0h1m17s