[2024-01-24 10:57:24,809] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:24,813] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:24,813] [INFO] DQC Reference Directory: /var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference
[2024-01-24 10:57:26,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:26,015] [INFO] Task started: Prodigal
[2024-01-24 10:57:26,015] [INFO] Running command: gunzip -c /var/lib/cwl/stgb001e04b-bed0-4d17-aa0d-ec67c8173135/GCF_024448495.1_ASM2444849v1_genomic.fna.gz | prodigal -d GCF_024448495.1_ASM2444849v1_genomic.fna/cds.fna -a GCF_024448495.1_ASM2444849v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:39,185] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:39,186] [INFO] Task started: HMMsearch
[2024-01-24 10:57:39,186] [INFO] Running command: hmmsearch --tblout GCF_024448495.1_ASM2444849v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference/reference_markers.hmm GCF_024448495.1_ASM2444849v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:39,527] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:39,529] [INFO] Found 6/6 markers.
[2024-01-24 10:57:39,567] [INFO] Query marker FASTA was written to GCF_024448495.1_ASM2444849v1_genomic.fna/markers.fasta
[2024-01-24 10:57:39,567] [INFO] Task started: Blastn
[2024-01-24 10:57:39,567] [INFO] Running command: blastn -query GCF_024448495.1_ASM2444849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference/reference_markers.fasta -out GCF_024448495.1_ASM2444849v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:40,615] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:40,618] [INFO] Selected 10 target genomes.
[2024-01-24 10:57:40,618] [INFO] Target genome list was writen to GCF_024448495.1_ASM2444849v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:40,632] [INFO] Task started: fastANI
[2024-01-24 10:57:40,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgb001e04b-bed0-4d17-aa0d-ec67c8173135/GCF_024448495.1_ASM2444849v1_genomic.fna.gz --refList GCF_024448495.1_ASM2444849v1_genomic.fna/target_genomes.txt --output GCF_024448495.1_ASM2444849v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:51,157] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:51,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:51,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:51,169] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:51,169] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:51,170] [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
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	100.0	1425	1427	95	conclusive
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	99.9885	1416	1427	95	conclusive
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	89.197	1209	1427	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_900114065.1	1211807	1211807	type	True	89.1561	1218	1427	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	89.1422	1222	1427	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	89.1292	1217	1427	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	89.1134	1175	1427	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	88.5339	1208	1427	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	88.5202	1184	1427	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	88.4351	1212	1427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:51,180] [INFO] DFAST Taxonomy check result was written to GCF_024448495.1_ASM2444849v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:51,181] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:51,181] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:51,181] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference/checkm_data
[2024-01-24 10:57:51,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:51,227] [INFO] Task started: CheckM
[2024-01-24 10:57:51,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024448495.1_ASM2444849v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024448495.1_ASM2444849v1_genomic.fna/checkm_input GCF_024448495.1_ASM2444849v1_genomic.fna/checkm_result
[2024-01-24 10:58:30,072] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:30,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:30,089] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:30,089] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:30,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024448495.1_ASM2444849v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:30,090] [INFO] Task started: Blastn
[2024-01-24 10:58:30,090] [INFO] Running command: blastn -query GCF_024448495.1_ASM2444849v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg045f51bf-5a15-46bc-b61d-a242b298a419/dqc_reference/reference_markers_gtdb.fasta -out GCF_024448495.1_ASM2444849v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:31,973] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:31,977] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:31,977] [INFO] Target genome list was writen to GCF_024448495.1_ASM2444849v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:32,020] [INFO] Task started: fastANI
[2024-01-24 10:58:32,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgb001e04b-bed0-4d17-aa0d-ec67c8173135/GCF_024448495.1_ASM2444849v1_genomic.fna.gz --refList GCF_024448495.1_ASM2444849v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024448495.1_ASM2444849v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:50,079] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:50,093] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:50,093] [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_003696315.1	s__Pseudomonas_A songnenensis	99.9885	1416	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	conclusive
GCF_000327065.1	s__Pseudomonas_A stutzeri_AE	93.1443	1334	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.70	97.56	0.93	0.91	3	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	90.1627	1252	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.44	99.44	0.92	0.92	2	-
GCF_014764705.1	s__Pseudomonas_A sp002692525	89.2381	1204	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0332	98.20	97.14	0.91	0.83	13	-
GCF_900114065.1	s__Pseudomonas_A kunmingensis	89.1667	1216	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.31	97.18	0.87	0.86	3	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	89.1419	1244	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	89.1262	1175	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	89.1231	1214	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	89.1203	1270	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCF_000935215.1	s__Pseudomonas_A stutzeri_AD	89.0184	1138	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.8359	97.48	96.93	0.86	0.84	3	-
GCF_000341615.1	s__Pseudomonas_A stutzeri_G	88.6927	1199	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.57	97.27	0.90	0.83	4	-
GCF_015291885.1	s__Pseudomonas_A stutzeri_AC	88.6465	1224	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.94	97.56	0.91	0.88	14	-
GCF_003205815.1	s__Pseudomonas_A sp003205815	88.4201	1253	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_002890795.1	s__Pseudomonas_A stutzeri_AA	88.2906	1258	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	86.5419	1108	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	86.1833	1092	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.7255	1052	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:50,095] [INFO] GTDB search result was written to GCF_024448495.1_ASM2444849v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:50,096] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:50,100] [INFO] DFAST_QC result json was written to GCF_024448495.1_ASM2444849v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:50,100] [INFO] DFAST_QC completed!
[2024-01-24 10:58:50,100] [INFO] Total running time: 0h1m25s