[2024-01-25 19:11:50,795] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:50,800] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:50,800] [INFO] DQC Reference Directory: /var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference
[2024-01-25 19:11:51,959] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:51,961] [INFO] Task started: Prodigal
[2024-01-25 19:11:51,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgadd94e89-333c-4086-ba64-db2244d9701e/GCF_014646595.1_ASM1464659v1_genomic.fna.gz | prodigal -d GCF_014646595.1_ASM1464659v1_genomic.fna/cds.fna -a GCF_014646595.1_ASM1464659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:07,247] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:07,247] [INFO] Task started: HMMsearch
[2024-01-25 19:12:07,248] [INFO] Running command: hmmsearch --tblout GCF_014646595.1_ASM1464659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference/reference_markers.hmm GCF_014646595.1_ASM1464659v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:07,587] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:07,588] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgadd94e89-333c-4086-ba64-db2244d9701e/GCF_014646595.1_ASM1464659v1_genomic.fna.gz]
[2024-01-25 19:12:07,637] [INFO] Query marker FASTA was written to GCF_014646595.1_ASM1464659v1_genomic.fna/markers.fasta
[2024-01-25 19:12:07,638] [INFO] Task started: Blastn
[2024-01-25 19:12:07,638] [INFO] Running command: blastn -query GCF_014646595.1_ASM1464659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference/reference_markers.fasta -out GCF_014646595.1_ASM1464659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:08,463] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:08,466] [INFO] Selected 13 target genomes.
[2024-01-25 19:12:08,466] [INFO] Target genome list was writen to GCF_014646595.1_ASM1464659v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:08,471] [INFO] Task started: fastANI
[2024-01-25 19:12:08,472] [INFO] Running command: fastANI --query /var/lib/cwl/stgadd94e89-333c-4086-ba64-db2244d9701e/GCF_014646595.1_ASM1464659v1_genomic.fna.gz --refList GCF_014646595.1_ASM1464659v1_genomic.fna/target_genomes.txt --output GCF_014646595.1_ASM1464659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:32,887] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:32,888] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:32,888] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:32,898] [WARNING] The ANI hits belong to more than one indistinguishable-group. The ANI hits will be classified as 'inconclusive,indistinguishable'. {}, {317: 'Pseudomonas syringae', 251699: 'Pseudomonas syringae group genomosp. 7', 251701: 'Pseudomonas syringae group genomosp. 3'}
[2024-01-25 19:12:32,898] [INFO] Found 13 fastANI hits (8 hits with ANI > threshold)
[2024-01-25 19:12:32,898] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:12:32,898] [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 avellanae	strain=JCM 11937	GCA_014646595.1	46257	46257	type	True	100.0	1816	1827	95	inconclusive
Pseudomonas avellanae	strain=BPIC 631	GCA_000444135.1	46257	46257	type	True	99.8929	1645	1827	95	inconclusive
Pseudomonas avellanae	strain=BPIC 631	GCA_000302915.1	46257	46257	type	True	99.6994	1789	1827	95	inconclusive
Pseudomonas syringae	strain=ICMP 9617	GCA_000658965.1	317	317	pathovar	True	97.3388	1634	1827	95	inconclusive
Pseudomonas syringae	strain=NCPPB 3739	GCA_000233835.2	317	317	pathovar	True	97.252	1369	1827	95	inconclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP529	GCA_001400335.1	251701	251701	pathovar	True	96.938	1491	1827	95	inconclusive
Pseudomonas syringae group genomosp. 3	strain=CFBP 1702	GCA_000935765.1	251701	251701	pathovar	True	96.7857	1642	1827	95	inconclusive
Pseudomonas syringae group genomosp. 3	strain=ICMP3963	GCA_001401175.1	251701	251701	pathovar	True	96.7263	1555	1827	95	inconclusive
Pseudomonas amygdali	strain=DSM 105780	GCA_022828345.1	47877	47877	pathovar	True	88.0258	1503	1827	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=LMG 5067	GCA_022557235.1	251699	251699	type	True	86.9255	1532	1827	95	below_threshold
Pseudomonas syringae group genomosp. 7	strain=ICMP 4091	GCA_022557255.1	251699	251699	pathovar	True	86.8059	1517	1827	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	80.1527	752	1827	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	80.1443	730	1827	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:32,899] [INFO] DFAST Taxonomy check result was written to GCF_014646595.1_ASM1464659v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:32,901] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:32,901] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:32,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference/checkm_data
[2024-01-25 19:12:32,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:32,961] [INFO] Task started: CheckM
[2024-01-25 19:12:32,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646595.1_ASM1464659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646595.1_ASM1464659v1_genomic.fna/checkm_input GCF_014646595.1_ASM1464659v1_genomic.fna/checkm_result
[2024-01-25 19:13:19,610] [INFO] Task succeeded: CheckM
[2024-01-25 19:13:19,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.05%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:13:19,641] [INFO] ===== Completeness check finished =====
[2024-01-25 19:13:19,641] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:13:19,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646595.1_ASM1464659v1_genomic.fna/markers.fasta)
[2024-01-25 19:13:19,642] [INFO] Task started: Blastn
[2024-01-25 19:13:19,642] [INFO] Running command: blastn -query GCF_014646595.1_ASM1464659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0db0f3c7-f0f6-4da6-a39a-189788571e94/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646595.1_ASM1464659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:13:21,231] [INFO] Task succeeded: Blastn
[2024-01-25 19:13:21,234] [INFO] Selected 11 target genomes.
[2024-01-25 19:13:21,234] [INFO] Target genome list was writen to GCF_014646595.1_ASM1464659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:13:21,242] [INFO] Task started: fastANI
[2024-01-25 19:13:21,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgadd94e89-333c-4086-ba64-db2244d9701e/GCF_014646595.1_ASM1464659v1_genomic.fna.gz --refList GCF_014646595.1_ASM1464659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646595.1_ASM1464659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:40,011] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:40,018] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:40,019] [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_000444135.1	s__Pseudomonas_E avellanae	99.88	1646	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.86	95.46	0.87	0.79	302	conclusive
GCF_002699855.1	s__Pseudomonas_E amygdali	87.9457	1412	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.09	96.47	0.89	0.82	226	-
GCF_900100365.1	s__Pseudomonas_E cannabina	87.5163	1487	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.50	95.44	0.90	0.84	17	-
GCF_001293775.1	s__Pseudomonas_E syringae_P	87.4904	1476	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.87	99.84	0.98	0.97	3	-
GCF_002093745.1	s__Pseudomonas_E graminis_C	87.4828	1433	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009176725.1	s__Pseudomonas_E syringae_M	87.1901	1458	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	98.71	98.38	0.92	0.88	59	-
GCF_900074915.1	s__Pseudomonas_E cerasi	87.1336	1527	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.51	98.33	0.88	0.83	51	-
GCF_000507185.2	s__Pseudomonas_E syringae	87.0383	1454	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0874	97.83	96.00	0.92	0.85	147	-
GCF_900103225.1	s__Pseudomonas_E congelans	87.0207	1434	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.60	98.04	0.95	0.92	20	-
GCF_001466965.1	s__Pseudomonas_E syringae_Q	86.9562	1449	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.91	98.87	0.94	0.94	3	-
GCF_000452705.1	s__Pseudomonas_E syringae_F	86.7717	1418	1827	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.97	98.97	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:40,020] [INFO] GTDB search result was written to GCF_014646595.1_ASM1464659v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:40,021] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:40,025] [INFO] DFAST_QC result json was written to GCF_014646595.1_ASM1464659v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:40,025] [INFO] DFAST_QC completed!
[2024-01-25 19:13:40,025] [INFO] Total running time: 0h1m49s