[2024-01-25 18:05:05,544] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:05:05,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:05:05,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference
[2024-01-25 18:05:06,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:05:06,693] [INFO] Task started: Prodigal
[2024-01-25 18:05:06,693] [INFO] Running command: gunzip -c /var/lib/cwl/stgaebe46c4-9f8d-4e1a-afbb-9f539b84a449/GCF_003797945.1_ASM379794v1_genomic.fna.gz | prodigal -d GCF_003797945.1_ASM379794v1_genomic.fna/cds.fna -a GCF_003797945.1_ASM379794v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:05:17,416] [INFO] Task succeeded: Prodigal
[2024-01-25 18:05:17,416] [INFO] Task started: HMMsearch
[2024-01-25 18:05:17,416] [INFO] Running command: hmmsearch --tblout GCF_003797945.1_ASM379794v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference/reference_markers.hmm GCF_003797945.1_ASM379794v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:05:17,637] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:05:17,638] [INFO] Found 6/6 markers.
[2024-01-25 18:05:17,672] [INFO] Query marker FASTA was written to GCF_003797945.1_ASM379794v1_genomic.fna/markers.fasta
[2024-01-25 18:05:17,673] [INFO] Task started: Blastn
[2024-01-25 18:05:17,673] [INFO] Running command: blastn -query GCF_003797945.1_ASM379794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference/reference_markers.fasta -out GCF_003797945.1_ASM379794v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:05:18,482] [INFO] Task succeeded: Blastn
[2024-01-25 18:05:18,484] [INFO] Selected 22 target genomes.
[2024-01-25 18:05:18,485] [INFO] Target genome list was writen to GCF_003797945.1_ASM379794v1_genomic.fna/target_genomes.txt
[2024-01-25 18:05:18,507] [INFO] Task started: fastANI
[2024-01-25 18:05:18,507] [INFO] Running command: fastANI --query /var/lib/cwl/stgaebe46c4-9f8d-4e1a-afbb-9f539b84a449/GCF_003797945.1_ASM379794v1_genomic.fna.gz --refList GCF_003797945.1_ASM379794v1_genomic.fna/target_genomes.txt --output GCF_003797945.1_ASM379794v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:05:34,243] [INFO] Task succeeded: fastANI
[2024-01-25 18:05:34,244] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:05:34,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:05:34,258] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:05:34,258] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:05:34,259] [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
Halopseudomonas pachastrellae	strain=JCM 12285	GCA_900114765.1	254161	254161	type	True	79.6846	570	1410	95	below_threshold
Halopseudomonas pachastrellae	strain=CCUG 46540	GCA_001989375.1	254161	254161	type	True	79.6203	561	1410	95	below_threshold
Halopseudomonas oceani	strain=CGMCC 1.15195	GCA_014641295.1	1708783	1708783	type	True	79.382	558	1410	95	below_threshold
Halopseudomonas oceani	strain=DSM 100277	GCA_002903165.1	1708783	1708783	type	True	79.3536	556	1410	95	below_threshold
Halopseudomonas aestusnigri	strain=CECT 8317	GCA_900108005.1	857252	857252	type	True	79.3402	572	1410	95	below_threshold
Halopseudomonas aestusnigri	strain=VGXO14	GCA_002197985.1	857252	857252	type	True	79.243	569	1410	95	below_threshold
Halopseudomonas litoralis	strain=2SM5	GCA_900105005.1	797277	797277	type	True	78.8045	311	1410	95	below_threshold
Halopseudomonas bauzanensis	strain=CGMCC 1.9095	GCA_900114735.1	653930	653930	type	True	78.682	321	1410	95	below_threshold
Halopseudomonas bauzanensis	strain=DSM 22558	GCA_900111225.1	653930	653930	type	True	78.6237	323	1410	95	below_threshold
Pseudomonas saliphila	strain=16W4-4-3	GCA_008638345.1	2586906	2586906	type	True	78.4929	333	1410	95	below_threshold
Pseudomonas profundi	strain=M5	GCA_008638305.1	1981513	1981513	type	True	78.3867	317	1410	95	below_threshold
Halopseudomonas salina	strain=CGMCC 1.12482	GCA_014637955.1	1323744	1323744	type	True	78.1847	324	1410	95	below_threshold
Halopseudomonas salina	strain=XCD-X85	GCA_008641105.1	1323744	1323744	type	True	78.0801	321	1410	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	77.5151	211	1410	95	below_threshold
Pseudomonas flexibilis	strain=ATCC 29606	GCA_900155995.1	706570	706570	type	True	77.431	155	1410	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	77.4072	193	1410	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	77.4071	234	1410	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	77.354	182	1410	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	77.3435	180	1410	95	below_threshold
Pseudomonas triticicola	strain=SWRI88	GCA_019145375.1	2842345	2842345	type	True	77.1607	159	1410	95	below_threshold
Pseudomonas zeshuii	strain=KACC 15471	GCA_900141925.1	1076620	1076620	type	True	76.7919	99	1410	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	76.0773	70	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:05:34,260] [INFO] DFAST Taxonomy check result was written to GCF_003797945.1_ASM379794v1_genomic.fna/tc_result.tsv
[2024-01-25 18:05:34,261] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:05:34,262] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:05:34,262] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference/checkm_data
[2024-01-25 18:05:34,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:05:34,309] [INFO] Task started: CheckM
[2024-01-25 18:05:34,309] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003797945.1_ASM379794v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003797945.1_ASM379794v1_genomic.fna/checkm_input GCF_003797945.1_ASM379794v1_genomic.fna/checkm_result
[2024-01-25 18:06:08,177] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:08,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:08,194] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:08,195] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:08,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003797945.1_ASM379794v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:08,196] [INFO] Task started: Blastn
[2024-01-25 18:06:08,196] [INFO] Running command: blastn -query GCF_003797945.1_ASM379794v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fd40b65-d0f1-4ddc-a44f-0be56729ccdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003797945.1_ASM379794v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:09,650] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:09,652] [INFO] Selected 18 target genomes.
[2024-01-25 18:06:09,653] [INFO] Target genome list was writen to GCF_003797945.1_ASM379794v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:09,663] [INFO] Task started: fastANI
[2024-01-25 18:06:09,663] [INFO] Running command: fastANI --query /var/lib/cwl/stgaebe46c4-9f8d-4e1a-afbb-9f539b84a449/GCF_003797945.1_ASM379794v1_genomic.fna.gz --refList GCF_003797945.1_ASM379794v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003797945.1_ASM379794v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:23,900] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:23,911] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:23,911] [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_003797905.1	s__Pseudomonas_D sp002683975	99.9986	1406	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.94	98.05	0.94	0.90	5	conclusive
GCF_900105255.1	s__Pseudomonas_D sabulinigri	81.5835	814	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053055.1	s__Pseudomonas_D sabulinigri_A	81.5546	786	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.96	99.96	0.96	0.96	2	-
GCF_900114765.1	s__Pseudomonas_D pachastrellae	79.6857	569	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.15	95.72	0.86	0.72	17	-
GCF_003444685.1	s__Pseudomonas_D gallaeciensis	79.5258	562	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.87	97.82	0.88	0.85	8	-
GCF_002197985.1	s__Pseudomonas_D aestusnigri	79.2518	569	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	97.11	96.74	0.91	0.81	25	-
GCF_009497895.1	s__Pseudomonas_D pelagia_A	79.2378	422	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000410875.1	s__Pseudomonas_D pelagia	78.8463	388	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105005.1	s__Pseudomonas_D litoralis	78.8371	308	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008365385.1	s__Pseudomonas_D laoshanensis	78.6977	384	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	96.00	95.95	0.96	0.95	3	-
GCF_900114735.1	s__Pseudomonas_D bauzanensis	78.6963	321	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	99.15	98.30	0.96	0.91	3	-
GCA_002840055.1	s__Pseudomonas_D sp002840055	78.6781	265	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000939975.1	s__Pseudomonas_D saudimassiliensis	78.4529	301	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014219065.1	s__Pseudomonas_D xiamenensis	78.2846	327	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115905.1	s__Pseudomonas_D formosensis	78.1716	279	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	98.74	98.74	0.94	0.94	2	-
GCA_019116555.1	s__Pseudomonas_D excrementavium	78.0741	234	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763285.1	s__Pseudomonas_D sp016763285	77.5513	252	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003208235.1	s__Pseudomonas_E sp003208235	77.0592	158	1410	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:23,913] [INFO] GTDB search result was written to GCF_003797945.1_ASM379794v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:23,914] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:23,918] [INFO] DFAST_QC result json was written to GCF_003797945.1_ASM379794v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:23,918] [INFO] DFAST_QC completed!
[2024-01-25 18:06:23,918] [INFO] Total running time: 0h1m18s