[2023-06-30 17:00:22,060] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:00:22,062] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:00:22,063] [INFO] DQC Reference Directory: /var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference
[2023-06-30 17:00:23,331] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:00:23,332] [INFO] Task started: Prodigal
[2023-06-30 17:00:23,332] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7fb4d47-a583-4d30-85c8-86c98d45b582/GCA_016765005.1_ASM1676500v1_genomic.fna.gz | prodigal -d GCA_016765005.1_ASM1676500v1_genomic.fna/cds.fna -a GCA_016765005.1_ASM1676500v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:26,599] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:26,600] [INFO] Task started: HMMsearch
[2023-06-30 17:00:26,600] [INFO] Running command: hmmsearch --tblout GCA_016765005.1_ASM1676500v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference/reference_markers.hmm GCA_016765005.1_ASM1676500v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:26,808] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:26,810] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb7fb4d47-a583-4d30-85c8-86c98d45b582/GCA_016765005.1_ASM1676500v1_genomic.fna.gz]
[2023-06-30 17:00:26,835] [INFO] Query marker FASTA was written to GCA_016765005.1_ASM1676500v1_genomic.fna/markers.fasta
[2023-06-30 17:00:26,835] [INFO] Task started: Blastn
[2023-06-30 17:00:26,835] [INFO] Running command: blastn -query GCA_016765005.1_ASM1676500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference/reference_markers.fasta -out GCA_016765005.1_ASM1676500v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:27,468] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:27,473] [INFO] Selected 12 target genomes.
[2023-06-30 17:00:27,473] [INFO] Target genome list was writen to GCA_016765005.1_ASM1676500v1_genomic.fna/target_genomes.txt
[2023-06-30 17:00:27,477] [INFO] Task started: fastANI
[2023-06-30 17:00:27,477] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7fb4d47-a583-4d30-85c8-86c98d45b582/GCA_016765005.1_ASM1676500v1_genomic.fna.gz --refList GCA_016765005.1_ASM1676500v1_genomic.fna/target_genomes.txt --output GCA_016765005.1_ASM1676500v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:00:35,698] [INFO] Task succeeded: fastANI
[2023-06-30 17:00:35,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:00:35,699] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:00:35,711] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:00:35,712] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:00:35,712] [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
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.0587	236	604	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.8598	221	604	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.7992	219	604	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.2613	149	604	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.1746	217	604	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.1569	172	604	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	77.7731	180	604	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:00:35,714] [INFO] DFAST Taxonomy check result was written to GCA_016765005.1_ASM1676500v1_genomic.fna/tc_result.tsv
[2023-06-30 17:00:35,715] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:00:35,715] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:00:35,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference/checkm_data
[2023-06-30 17:00:35,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:00:35,743] [INFO] Task started: CheckM
[2023-06-30 17:00:35,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016765005.1_ASM1676500v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016765005.1_ASM1676500v1_genomic.fna/checkm_input GCA_016765005.1_ASM1676500v1_genomic.fna/checkm_result
[2023-06-30 17:00:53,759] [INFO] Task succeeded: CheckM
[2023-06-30 17:00:53,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.93%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 17:00:53,784] [INFO] ===== Completeness check finished =====
[2023-06-30 17:00:53,784] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:00:53,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016765005.1_ASM1676500v1_genomic.fna/markers.fasta)
[2023-06-30 17:00:53,785] [INFO] Task started: Blastn
[2023-06-30 17:00:53,785] [INFO] Running command: blastn -query GCA_016765005.1_ASM1676500v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg00963987-84de-475b-b633-783005d27a24/dqc_reference/reference_markers_gtdb.fasta -out GCA_016765005.1_ASM1676500v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:54,699] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:54,705] [INFO] Selected 12 target genomes.
[2023-06-30 17:00:54,705] [INFO] Target genome list was writen to GCA_016765005.1_ASM1676500v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:00:54,735] [INFO] Task started: fastANI
[2023-06-30 17:00:54,735] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7fb4d47-a583-4d30-85c8-86c98d45b582/GCA_016765005.1_ASM1676500v1_genomic.fna.gz --refList GCA_016765005.1_ASM1676500v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016765005.1_ASM1676500v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:01:03,356] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:03,371] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 17:01:03,372] [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
GCA_013215465.1	s__Colwellia sp013215465	93.2911	549	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_003333305.1	s__Colwellia aromaticivorans	85.4738	454	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	85.2826	457	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_003521815.1	s__Colwellia sp003521815	83.8135	336	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162675.1	s__Colwellia sp002162675	79.4214	275	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	79.3641	219	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	79.3303	201	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	78.9292	219	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_000378625.1	s__Colwellia piezophila	78.9	218	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002207865.1	s__Colwellia marinimaniae	78.8399	217	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	78.8239	203	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.4054	175	604	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 17:01:03,374] [INFO] GTDB search result was written to GCA_016765005.1_ASM1676500v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:01:03,374] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:01:03,378] [INFO] DFAST_QC result json was written to GCA_016765005.1_ASM1676500v1_genomic.fna/dqc_result.json
[2023-06-30 17:01:03,378] [INFO] DFAST_QC completed!
[2023-06-30 17:01:03,378] [INFO] Total running time: 0h0m41s