[2024-01-24 14:05:31,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference
[2024-01-24 14:05:32,510] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,511] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,511] [INFO] Running command: gunzip -c /var/lib/cwl/stg523fe967-4258-4236-8dbd-f005dd83ada5/GCF_002843355.2_ASM284335v2_genomic.fna.gz | prodigal -d GCF_002843355.2_ASM284335v2_genomic.fna/cds.fna -a GCF_002843355.2_ASM284335v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:39,857] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:39,858] [INFO] Task started: HMMsearch
[2024-01-24 14:05:39,858] [INFO] Running command: hmmsearch --tblout GCF_002843355.2_ASM284335v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference/reference_markers.hmm GCF_002843355.2_ASM284335v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:40,139] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:40,141] [INFO] Found 6/6 markers.
[2024-01-24 14:05:40,176] [INFO] Query marker FASTA was written to GCF_002843355.2_ASM284335v2_genomic.fna/markers.fasta
[2024-01-24 14:05:40,176] [INFO] Task started: Blastn
[2024-01-24 14:05:40,176] [INFO] Running command: blastn -query GCF_002843355.2_ASM284335v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference/reference_markers.fasta -out GCF_002843355.2_ASM284335v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:40,884] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:40,887] [INFO] Selected 13 target genomes.
[2024-01-24 14:05:40,887] [INFO] Target genome list was writen to GCF_002843355.2_ASM284335v2_genomic.fna/target_genomes.txt
[2024-01-24 14:05:40,910] [INFO] Task started: fastANI
[2024-01-24 14:05:40,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg523fe967-4258-4236-8dbd-f005dd83ada5/GCF_002843355.2_ASM284335v2_genomic.fna.gz --refList GCF_002843355.2_ASM284335v2_genomic.fna/target_genomes.txt --output GCF_002843355.2_ASM284335v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:51,324] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:51,324] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:51,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:51,332] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:51,332] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:51,332] [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 echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	100.0	1368	1371	95	conclusive
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.9128	553	1371	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	79.7259	482	1371	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	79.5065	487	1371	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	79.0851	478	1371	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.4741	299	1371	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.357	215	1371	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:51,334] [INFO] DFAST Taxonomy check result was written to GCF_002843355.2_ASM284335v2_genomic.fna/tc_result.tsv
[2024-01-24 14:05:51,335] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:51,335] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:51,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference/checkm_data
[2024-01-24 14:05:51,336] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:51,383] [INFO] Task started: CheckM
[2024-01-24 14:05:51,384] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002843355.2_ASM284335v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002843355.2_ASM284335v2_genomic.fna/checkm_input GCF_002843355.2_ASM284335v2_genomic.fna/checkm_result
[2024-01-24 14:06:18,473] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:18,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:18,491] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:18,492] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:18,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002843355.2_ASM284335v2_genomic.fna/markers.fasta)
[2024-01-24 14:06:18,492] [INFO] Task started: Blastn
[2024-01-24 14:06:18,492] [INFO] Running command: blastn -query GCF_002843355.2_ASM284335v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d6526b5-a2af-4659-b653-5af175a51282/dqc_reference/reference_markers_gtdb.fasta -out GCF_002843355.2_ASM284335v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:19,552] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:19,556] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:19,556] [INFO] Target genome list was writen to GCF_002843355.2_ASM284335v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:19,570] [INFO] Task started: fastANI
[2024-01-24 14:06:19,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg523fe967-4258-4236-8dbd-f005dd83ada5/GCF_002843355.2_ASM284335v2_genomic.fna.gz --refList GCF_002843355.2_ASM284335v2_genomic.fna/target_genomes_gtdb.txt --output GCF_002843355.2_ASM284335v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:31,249] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:31,260] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:31,261] [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_002843355.2	s__Colwellia echini	100.0	1368	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860585.1	s__Colwellia sp018860585	82.2188	824	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	79.913	571	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	79.9036	554	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545415.1	s__Colwellia sp003545415	79.7848	434	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	79.738	482	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764225.1	s__Colwellia psychrerythraea_D	79.6727	499	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	79.6646	555	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	79.5777	471	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860755.1	s__Colwellia sp018860755	79.38	364	1371	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	78.3126	304	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.9696	237	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.6222	215	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765535.1	s__GCA-2401725 sp016765535	77.5841	199	1371	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:31,265] [INFO] GTDB search result was written to GCF_002843355.2_ASM284335v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:31,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:31,270] [INFO] DFAST_QC result json was written to GCF_002843355.2_ASM284335v2_genomic.fna/dqc_result.json
[2024-01-24 14:06:31,271] [INFO] DFAST_QC completed!
[2024-01-24 14:06:31,271] [INFO] Total running time: 0h0m60s